[ Started: 2026-02-08 03:09:55 CET ]
[ OmnipathR v3.16.2 for BioC-3.21 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_21 (e923fc4 2025-08-30 11:55:56) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-02-08 03:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:10:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:10:11] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:10:11] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpxhl7yy/Rinst3963171144b53d/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpxhl7yy/Rinst3963171144b53d/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpxhl7yy/Rinst3963171144b53d/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpxhl7yy/Rinst3963171144b53d/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2026-02-08 03:10:11] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:11] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:11] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:16] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:21] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:10:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:10:21] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:10:21] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from bioc_workshop.Rmd:215-218 [network]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─OmnipathR::transcriptional()
  2. │ ├─rlang::exec(omnipath_query, !!!args)
  3. │ └─OmnipathR (local) `<fn>`(...)
  4. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
  5. ├─OmnipathR:::omnipath_check_param(.)
  6. │ └─param$organisms %<>% map_int(ncbi_taxid)
  7. ├─purrr::map_int(., ncbi_taxid)
  8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  9. │   ├─purrr:::with_indexed_errors(...)
 10. │   │ └─base::withCallingHandlers(...)
 11. │   ├─purrr:::call_with_cleanup(...)
 12. │   └─OmnipathR (local) .f(.x[[i]], ...)
 13. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 14. ├─purrr::map_int(., taxon_name, "ncbi")
 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. │     ├─... %>% if_null_len0(NA)
 21. │     └─OmnipathR::get_db("organisms")
 22. │       └─OmnipathR::load_db(key, param = param)
 23. │         ├─rlang::exec(loader, !!!param)
 24. │         └─OmnipathR (local) `<fn>`()
 25. │           ├─... %>% ...
 26. │           └─OmnipathR::ensembl_organisms()
 27. │             ├─... %>% ...
 28. │             └─OmnipathR::ensembl_organisms_raw()
 29. │               └─... %>% html_table()
 30. ├─OmnipathR:::if_null_len0(., NA)
 31. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 32. ├─OmnipathR:::is_empty_2(.)
 33. │ └─value %>% ...
 34. ├─dplyr::first(.)
 35. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 36. │   └─vctrs::vec_size(x)
 37. ├─dplyr::pull(., name_type)
 38. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 39. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 40. ├─dplyr::mutate(...)
 41. ├─dplyr::full_join(...)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::select(...)
 44. ├─rvest::html_table(.)
 45. ├─rvest::html_element(., "table")
 46. ├─xml2::read_html(.)
 47. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 48.   └─OmnipathR:::download_base(...)
 49.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-02-08 03:10:22] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:10:22] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:22] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2026-02-08 03:10:22] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:22] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:22] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:27] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:27] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:32] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:32] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:10:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:10:32] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:10:33] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─OmnipathR::omnipath_for_cosmos()
  2. │ └─organism %<>% organism_for("omnipath")
  3. ├─OmnipathR::organism_for(., "omnipath")
  4. │ └─get(resource_info$check_by_id)(organism)
  5. │   └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
  6. ├─purrr::map_int(., taxon_name, "ncbi")
  7. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  8. │   ├─purrr:::with_indexed_errors(...)
  9. │   │ └─base::withCallingHandlers(...)
 10. │   ├─purrr:::call_with_cleanup(...)
 11. │   └─OmnipathR (local) .f(.x[[i]], ...)
 12. │     ├─... %>% if_null_len0(NA)
 13. │     └─OmnipathR::get_db("organisms")
 14. │       └─OmnipathR::load_db(key, param = param)
 15. │         ├─rlang::exec(loader, !!!param)
 16. │         └─OmnipathR (local) `<fn>`()
 17. │           ├─... %>% ...
 18. │           └─OmnipathR::ensembl_organisms()
 19. │             ├─... %>% ...
 20. │             └─OmnipathR::ensembl_organisms_raw()
 21. │               └─... %>% html_table()
 22. ├─OmnipathR:::if_null_len0(., NA)
 23. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 24. ├─OmnipathR:::is_empty_2(.)
 25. │ └─value %>% ...
 26. ├─dplyr::first(.)
 27. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 28. │   └─vctrs::vec_size(x)
 29. ├─dplyr::pull(., name_type)
 30. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 31. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 32. ├─dplyr::mutate(...)
 33. ├─dplyr::full_join(...)
 34. ├─dplyr::mutate(...)
 35. ├─dplyr::select(...)
 36. ├─rvest::html_table(.)
 37. ├─rvest::html_element(., "table")
 38. ├─xml2::read_html(.)
 39. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 40.   └─OmnipathR:::download_base(...)
 41.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2026-02-08 03:10:33] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:33] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:38] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:43] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:43] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:10:43] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:10:43] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:10:43] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:10:43] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:10:44] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:10:44] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:10:44] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:10:44] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from db_manager.Rmd:66-69 [get]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─OmnipathR::get_db("up_gs")
  2. │ └─OmnipathR::load_db(key, param = param)
  3. │   ├─rlang::exec(loader, !!!param)
  4. │   └─OmnipathR (local) `<fn>`(to = "genesymbol", organism = 9606L)
  5. │     └─... %>% trim_and_distinct
  6. ├─OmnipathR:::trim_and_distinct(.)
  7. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
  8. ├─dplyr::distinct(.)
  9. ├─dplyr::mutate(., across(everything(), str_trim))
 10. ├─dplyr::filter(., !is.na(From) & !is.na(To))
 11. ├─tidyr::separate_rows(., To, sep = "[; ]")
 12. ├─tidyr::separate_rows(., From, sep = "[; ]")
 13. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To))
 14. ├─dplyr::rename(., From = 1, To = 2)
 15. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism)
 16. │ └─organism %<>% ncbi_taxid
 17. ├─OmnipathR::ncbi_taxid(.)
 18. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 19. ├─purrr::map_int(., taxon_name, "ncbi")
 20. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 21. │   ├─purrr:::with_indexed_errors(...)
 22. │   │ └─base::withCallingHandlers(...)
 23. │   ├─purrr:::call_with_cleanup(...)
 24. │   └─OmnipathR (local) .f(.x[[i]], ...)
 25. │     ├─... %>% if_null_len0(NA)
 26. │     └─OmnipathR::get_db("organisms")
 27. │       └─OmnipathR::load_db(key, param = param)
 28. │         ├─rlang::exec(loader, !!!param)
 29. │         └─OmnipathR (local) `<fn>`()
 30. │           ├─... %>% ...
 31. │           └─OmnipathR::ensembl_organisms()
 32. │             ├─... %>% ...
 33. │             └─OmnipathR::ensembl_organisms_raw()
 34. │               └─... %>% html_table()
 35. ├─OmnipathR:::if_null_len0(., NA)
 36. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 37. ├─OmnipathR:::is_empty_2(.)
 38. │ └─value %>% ...
 39. ├─dplyr::first(.)
 40. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 41. │   └─vctrs::vec_size(x)
 42. ├─dplyr::pull(., name_type)
 43. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 44. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 45. ├─dplyr::mutate(...)
 46. ├─dplyr::full_join(...)
 47. ├─dplyr::mutate(...)
 48. ├─dplyr::select(...)
 49. ├─rvest::html_table(.)
 50. ├─rvest::html_element(., "table")
 51. ├─xml2::read_html(.)
 52. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 53.   └─OmnipathR:::download_base(...)
 54.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-08 03:10:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:10:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:45] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2026-02-08 03:10:45] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:45] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:45] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:50] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:50] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:55] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:55] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:10:55] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:10:55] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:10:56] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggforce 0.5.0(2025-06-18); ggplot2 4.0.2(2026-02-03); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:10:56] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─omnipath() %>% as_tibble()
  2. ├─tibble::as_tibble(.)
  3. ├─OmnipathR::omnipath()
  4. │ ├─rlang::exec(omnipath_interactions, !!!args)
  5. │ └─OmnipathR (local) `<fn>`(datasets = "omnipath")
  6. │   ├─rlang::exec(omnipath_query, !!!args)
  7. │   └─OmnipathR (local) `<fn>`(datasets = "omnipath", query_type = "interactions")
  8. │     └─environment() %>% as.list %>% c(list(...)) %>% ...
  9. ├─OmnipathR:::omnipath_check_param(.)
 10. │ └─param$organisms %<>% map_int(ncbi_taxid)
 11. ├─purrr::map_int(., ncbi_taxid)
 12. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 13. │   ├─purrr:::with_indexed_errors(...)
 14. │   │ └─base::withCallingHandlers(...)
 15. │   ├─purrr:::call_with_cleanup(...)
 16. │   └─OmnipathR (local) .f(.x[[i]], ...)
 17. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 18. ├─purrr::map_int(., taxon_name, "ncbi")
 19. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 20. │   ├─purrr:::with_indexed_errors(...)
 21. │   │ └─base::withCallingHandlers(...)
 22. │   ├─purrr:::call_with_cleanup(...)
 23. │   └─OmnipathR (local) .f(.x[[i]], ...)
 24. │     ├─... %>% if_null_len0(NA)
 25. │     └─OmnipathR::get_db("organisms")
 26. │       └─OmnipathR::load_db(key, param = param)
 27. │         ├─rlang::exec(loader, !!!param)
 28. │         └─OmnipathR (local) `<fn>`()
 29. │           ├─... %>% ...
 30. │           └─OmnipathR::ensembl_organisms()
 31. │             ├─... %>% ...
 32. │             └─OmnipathR::ensembl_organisms_raw()
 33. │               └─... %>% html_table()
 34. ├─OmnipathR:::if_null_len0(., NA)
 35. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 36. ├─OmnipathR:::is_empty_2(.)
 37. │ └─value %>% ...
 38. ├─dplyr::first(.)
 39. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 40. │   └─vctrs::vec_size(x)
 41. ├─dplyr::pull(., name_type)
 42. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 43. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 44. ├─dplyr::mutate(...)
 45. ├─dplyr::full_join(...)
 46. ├─dplyr::mutate(...)
 47. ├─dplyr::select(...)
 48. ├─rvest::html_table(.)
 49. ├─rvest::html_element(., "table")
 50. ├─xml2::read_html(.)
 51. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 52.   └─OmnipathR:::download_base(...)
 53.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-02-08 03:10:56] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:10:56] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:10:56] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2026-02-08 03:10:56] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:10:56] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:10:57] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:02] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:02] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:07] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:11:07] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:11:07] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggforce 0.5.0(2025-06-18); ggplot2 4.0.2(2026-02-03); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:11:07] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from extra_attrs.Rmd:55-58 [load-interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─OmnipathR::post_translational(fields = "extra_attrs")
  2. │ ├─rlang::exec(omnipath_query, !!!args)
  3. │ └─OmnipathR (local) `<fn>`(fields = "extra_attrs", query_type = "interactions", datasets = `<chr>`)
  4. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
  5. ├─OmnipathR:::omnipath_check_param(.)
  6. │ └─param$organisms %<>% map_int(ncbi_taxid)
  7. ├─purrr::map_int(., ncbi_taxid)
  8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
  9. │   ├─purrr:::with_indexed_errors(...)
 10. │   │ └─base::withCallingHandlers(...)
 11. │   ├─purrr:::call_with_cleanup(...)
 12. │   └─OmnipathR (local) .f(.x[[i]], ...)
 13. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 14. ├─purrr::map_int(., taxon_name, "ncbi")
 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. │     ├─... %>% if_null_len0(NA)
 21. │     └─OmnipathR::get_db("organisms")
 22. │       └─OmnipathR::load_db(key, param = param)
 23. │         ├─rlang::exec(loader, !!!param)
 24. │         └─OmnipathR (local) `<fn>`()
 25. │           ├─... %>% ...
 26. │           └─OmnipathR::ensembl_organisms()
 27. │             ├─... %>% ...
 28. │             └─OmnipathR::ensembl_organisms_raw()
 29. │               └─... %>% html_table()
 30. ├─OmnipathR:::if_null_len0(., NA)
 31. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 32. ├─OmnipathR:::is_empty_2(.)
 33. │ └─value %>% ...
 34. ├─dplyr::first(.)
 35. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 36. │   └─vctrs::vec_size(x)
 37. ├─dplyr::pull(., name_type)
 38. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 39. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 40. ├─dplyr::mutate(...)
 41. ├─dplyr::full_join(...)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::select(...)
 44. ├─rvest::html_table(.)
 45. ├─rvest::html_element(., "table")
 46. ├─xml2::read_html(.)
 47. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 48.   └─OmnipathR:::download_base(...)
 49.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-02-08 03:11:09] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:11:09] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:11:09] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2026-02-08 03:11:09] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:09] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:19] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:11:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:11:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:11:20] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggforce 0.5.0(2025-06-18); ggplot2 4.0.2(2026-02-03); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gprofiler2 0.2.4(2025-11-11); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:11:20] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from omnipath_intro.Rmd:166-175 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─OmnipathR::omnipath(...)
  2. │ ├─rlang::exec(omnipath_interactions, !!!args)
  3. │ └─OmnipathR (local) `<fn>`(resources = `<chr>`, datasets = "omnipath")
  4. │   ├─rlang::exec(omnipath_query, !!!args)
  5. │   └─OmnipathR (local) `<fn>`(datasets = "omnipath", resources = `<chr>`, query_type = "interactions")
  6. │     └─environment() %>% as.list %>% c(list(...)) %>% ...
  7. ├─OmnipathR:::omnipath_check_param(.)
  8. │ └─param$organisms %<>% map_int(ncbi_taxid)
  9. ├─purrr::map_int(., ncbi_taxid)
 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 11. │   ├─purrr:::with_indexed_errors(...)
 12. │   │ └─base::withCallingHandlers(...)
 13. │   ├─purrr:::call_with_cleanup(...)
 14. │   └─OmnipathR (local) .f(.x[[i]], ...)
 15. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 16. ├─purrr::map_int(., taxon_name, "ncbi")
 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 18. │   ├─purrr:::with_indexed_errors(...)
 19. │   │ └─base::withCallingHandlers(...)
 20. │   ├─purrr:::call_with_cleanup(...)
 21. │   └─OmnipathR (local) .f(.x[[i]], ...)
 22. │     ├─... %>% if_null_len0(NA)
 23. │     └─OmnipathR::get_db("organisms")
 24. │       └─OmnipathR::load_db(key, param = param)
 25. │         ├─rlang::exec(loader, !!!param)
 26. │         └─OmnipathR (local) `<fn>`()
 27. │           ├─... %>% ...
 28. │           └─OmnipathR::ensembl_organisms()
 29. │             ├─... %>% ...
 30. │             └─OmnipathR::ensembl_organisms_raw()
 31. │               └─... %>% html_table()
 32. ├─OmnipathR:::if_null_len0(., NA)
 33. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 34. ├─OmnipathR:::is_empty_2(.)
 35. │ └─value %>% ...
 36. ├─dplyr::first(.)
 37. │ └─dplyr::nth(x, 1L, order_by = order_by, default = default, na_rm = na_rm)
 38. │   └─vctrs::vec_size(x)
 39. ├─dplyr::pull(., name_type)
 40. ├─dplyr::filter(., if_any(ends_with("_l"), ~.x == name))
 41. ├─dplyr::select(., -latin_name.x, -latin_name.y)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::full_join(...)
 44. ├─dplyr::mutate(...)
 45. ├─dplyr::select(...)
 46. ├─rvest::html_table(.)
 47. ├─rvest::html_element(., "table")
 48. ├─xml2::read_html(.)
 49. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 50.   └─OmnipathR:::download_base(...)
 51.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-02-08 03:11:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-08 03:11:20] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-08 03:11:20] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2026-02-08 03:11:20] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:25] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:25] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:30] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-08 03:11:31] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-08 03:11:31] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-08 02:09:56 UTC; unix
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-08; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-08 03:11:31] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-08 03:11:31] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggforce 0.5.0(2025-06-18); ggplot2 4.0.2(2026-02-03); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gprofiler2 0.2.4(2025-11-11); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2026-02-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-08 03:11:31] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from paths.Rmd:55-67 [tfcensus-op]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map_int()`:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
---
Backtrace:
     ▆
  1. ├─... %>% unique
  2. ├─base::unique(.)
  3. ├─dplyr::pull(., genesymbol)
  4. ├─OmnipathR::annotations(resources = "TFcensus", entity_types = "protein")
  5. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args)
  6. │ └─OmnipathR (local) `<fn>`(...)
  7. │   └─environment() %>% as.list %>% c(list(...)) %>% ...
  8. ├─OmnipathR:::omnipath_check_param(.)
  9. │ └─param$organisms %<>% map_int(ncbi_taxid)
 10. ├─purrr::map_int(., ncbi_taxid)
 11. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   ├─purrr:::call_with_cleanup(...)
 15. │   └─OmnipathR (local) .f(.x[[i]], ...)
 16. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 17. ├─purrr::map_int(., taxon_name, "ncbi")
 18. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 19. │   ├─purrr:::with_indexed_errors(...)
 20. │   │ └─base::withCallingHandlers(...)
 21. │   ├─purrr:::call_with_cleanup(...)
 22. │   └─OmnipathR (local) .f(.x[[i]], ...)
 23. │     ├─... %>% if_null_len0(NA)
 24. │     └─OmnipathR::get_db("organisms")
 25. │       └─OmnipathR::load_db(key, param = param)
 26. │         ├─rlang::exec(loader, !!!param)
 27. │         └─OmnipathR (local) `<fn>`()
 28. │           ├─... %>% ...
 29. │           └─OmnipathR::ensembl_organisms()
 30. │             ├─... %>% ...
 31. │             └─OmnipathR::ensembl_organisms_raw()
 32. │               └─... %>% html_table()
 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::mutate(...)
 46. ├─dplyr::select(...)
 47. ├─rvest::html_table(.)
 48. ├─rvest::html_element(., "table")
 49. ├─xml2::read_html(.)
 50. └─OmnipathR:::download_to_cache(., http_headers = user_agent())
 51.   └─OmnipathR:::download_base(...)
 52.     └─base::stop(result)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'paths.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform1()`:
! unused arguments (req_prep, resend_count = n)
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’
  ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2026-02-08 03:11:32 CET ]