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This page was generated on 2025-12-11 12:05 -0500 (Thu, 11 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4670
kjohnson1macOS 13.7.5 Venturaarm644.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" 4604
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4669
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1505/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.18.2  (landing page)
Denes Turei
Snapshot Date: 2025-12-08 13:45 -0500 (Mon, 08 Dec 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_22
git_last_commit: 7ab5630
git_last_commit_date: 2025-11-17 12:48:40 -0500 (Mon, 17 Nov 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
merida1macOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.7.5 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

BUILD results for OmnipathR on merida1

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OmnipathR
Version: 3.18.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2025-12-08 21:55:21 -0500 (Mon, 08 Dec 2025)
EndedAt: 2025-12-08 21:59:36 -0500 (Mon, 08 Dec 2025)
EllapsedTime: 255.5 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/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
[2025-12-08 21:56:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:56:24] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:56:25] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:56:25] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:56:25] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpmnI6iQ/Rinst1781613587e2d/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpmnI6iQ/Rinst1781613587e2d/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpmnI6iQ/Rinst1781613587e2d/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpmnI6iQ/Rinst1781613587e2d/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:25] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-12-08 21:56:26] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:26] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:26] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-12-08 21:56:26] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:26] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:31] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:31] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:36] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:56:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:56:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:56:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:56:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:56:37] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:56:37] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:56:37] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:56:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:56:38] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:56:38] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:56:38] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:56:38] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:56:38] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:56:38] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:56:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:38] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 2.
[2025-12-08 21:56:38] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-2.html
[2025-12-08 21:56:38] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:39] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:39] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:44] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:44] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:49] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:56:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:56:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:56:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:56:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:56:50] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:56:50] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:56:50] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:56:50] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from bioc_workshop.Rmd:215-218 [network]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:56:51] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-12-08 21:56:51] [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.
[2025-12-08 21:56:51] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-12-08 21:56:51] [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.
[2025-12-08 21:56:51] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-12-08 21:56:51] [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.
[2025-12-08 21:56:52] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:56:52] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:56:52] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 3.
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-3.html
[2025-12-08 21:56:52] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:52] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:52] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:56:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:56:57] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:02] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:02] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:02] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:02] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:02] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:02] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:02] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:03] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:03] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:03] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:03] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:04] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:04] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:04] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:04] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:57:04] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:57:04] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 4.
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-4.html
[2025-12-08 21:57:04] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:05] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:10] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:15] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:15] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:16] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:16] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:16] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:16] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:57:17] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-12-08 21:57:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:57:17] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:57:17] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 5.
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-5.html
[2025-12-08 21:57:17] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:17] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:22] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:22] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:27] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:27] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:28] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:28] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:28] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:28] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:29] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:29] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:30] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:30] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:57:30] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:57:30] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 6.
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-6.html
[2025-12-08 21:57:30] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:30] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:30] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:35] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:35] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:40] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:40] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:40] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:40] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:40] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:40] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:40] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:41] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:41] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:41] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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 1.1.4(2023-11-17); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:41] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from db_manager.Rmd:66-69 [get]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-12-08 21:57:44] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:57:44] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:57:44] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 7.
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-7.html
[2025-12-08 21:57:44] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:44] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:44] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:49] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:54] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:54] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:57:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:55] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:55] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:55] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:55] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:56] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:57:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:57:56] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:57:57] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:57:57] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:57:57] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:57:57] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 8.
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-8.html
[2025-12-08 21:57:57] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:57:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:57:57] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:02] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:02] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:07] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:08] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:08] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:09] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:09] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-12-08 21:58:09] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:58:09] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:58:09] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 9.
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-9.html
[2025-12-08 21:58:09] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:10] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:15] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:15] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:20] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:21] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:21] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:58:21] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:21] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:22] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:22] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:23] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:23] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:58:23] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:58:23] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 10.
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-10.html
[2025-12-08 21:58:23] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:23] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:23] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:28] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:33] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:34] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:34] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:34] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); 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); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:34] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from extra_attrs.Rmd:55-58 [load-interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:58:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-12-08 21:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-12-08 21:58:41] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:58:41] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:58:41] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 11.
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-11.html
[2025-12-08 21:58:41] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:41] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:41] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:46] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:46] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:51] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:52] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:52] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:52] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:58:53] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:58:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:58:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:58:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:58:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:58:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:58:54] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:58:54] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:58:54] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:58:54] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:58:54] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:58:54] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 12.
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-12.html
[2025-12-08 21:58:54] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:58:54] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:58:54] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:58:59] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:58:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:00] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:00] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:00] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:00] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:05] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:59:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:59:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:59:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:59:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:59:06] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:59:06] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:59:06] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:59:06] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from omnipath_intro.Rmd:166-175 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-12-08 21:59:07] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 21:59:07] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:59:07] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 13.
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-13.html
[2025-12-08 21:59:07] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:07] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:12] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:12] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:17] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:59:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:59:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:59:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:59:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:59:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:59:19] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:59:20] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:59:20] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:59:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:59:22] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:59:22] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:59:22] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:59:22] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-12-08 21:59:22] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 21:59:22] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 21:59:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 21:59:23] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 14.
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-14.html
[2025-12-08 21:59:23] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:23] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:23] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:28] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 21:59:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 21:59:33] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n)
[2025-12-08 21:59:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 21:59:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 21:59:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 02:55:25 UTC; unix
[2025-12-08 21:59:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 21:59:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 21:59:34] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-12-08 21:59:34] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-12-08 21:59:34] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); 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 4.0.1(2025-11-14); 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 1.50(2025-03-16); later 1.4.4(2025-08-27); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-12-08); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); 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 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tweenr 2.0.3(2024-02-26); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-08 21:59:34] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from paths.Rmd:55-67 [tfcensus-op]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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