Multiple platform build/check report for BioC 3.22 - BUILD results for OmnipathR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4670
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4604
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (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*
BUILD results for OmnipathR on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmnipathR
StartedAt: 2025-12-08 19:10:15 -0500 (Mon, 08 Dec 2025)
EndedAt: 2025-12-08 19:13:26 -0500 (Mon, 08 Dec 2025)
EllapsedTime: 191.2 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 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 19:10:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:10:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:10:36] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:10:36] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:10:36] [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 19:10:36] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpru6onm/Rinst24610e366b0ea9/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpru6onm/Rinst24610e366b0ea9/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpru6onm/Rinst24610e366b0ea9/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmpru6onm/Rinst24610e366b0ea9/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-12-08 19:10:36] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:36] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-12-08 19:10:36] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:36] [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 19:10:41] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:41] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:41] [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 19:10:46] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:46] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:46] [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 19:10:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:10:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:10:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:10:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:10:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:10:46] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:10:46] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:10:47] [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 19:10:47] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:10:47] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:10:47] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:10:47] [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 19:10:47] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 2.
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-2.html
[2025-12-08 19:10:47] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:47] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:47] [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 19:10:52] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:52] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:52] [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 19:10:57] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:57] [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 19:10:57] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:10:57] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:10:57] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:10:57] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:10:57] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:10:58] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:10:58] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:10:58] [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 19:10:58] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from bioc_workshop.Rmd:215-218 [network]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:10:58] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-12-08 19:10:58] [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 19:10:58] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-12-08 19:10:58] [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 19:10:58] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-12-08 19:10:58] [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 19:10:58] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:10:58] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:10:58] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 3.
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-3.html
[2025-12-08 19:10:58] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:10:58] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:10:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:10:59] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:10:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:10:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:10:59] [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 19:11:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:04] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:04] [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 19:11:09] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:09] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:09] [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 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:09] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:09] [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); 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 19:11:09] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:09] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:10] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:10] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:10] [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 19:11:10] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:11:10] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:11:10] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 4.
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-4.html
[2025-12-08 19:11:10] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:10] [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 19:11:15] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:15] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:15] [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 19:11:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:20] [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 19:11:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:20] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:20] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); 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 19:11:20] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:11:21] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2025-12-08 19:11:21] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:11:21] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:11:21] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 5.
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-5.html
[2025-12-08 19:11:21] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:21] [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 19:11:26] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:26] [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 19:11:31] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:31] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:31] [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 19:11:31] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:31] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:31] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-12-08); 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 19:11:31] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:32] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:32] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:32] [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 19:11:32] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 6.
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-6.html
[2025-12-08 19:11:32] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:32] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:32] [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 19:11:37] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:37] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:37] [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 19:11:42] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:42] [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 19:11:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:43] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:43] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:43] [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 19:11:43] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from db_manager.Rmd:66-69 [get]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:11:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2025-12-08 19:11:44] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:11:44] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:11:44] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 7.
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-7.html
[2025-12-08 19:11:44] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:44] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:44] [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 19:11:49] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:49] [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 19:11:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:54] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:54] [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 19:11:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:55] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:55] [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 19:11:55] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:55] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:11:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:11:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:11:56] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:11:56] [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 19:11:56] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:11:56] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:11:56] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 8.
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-8.html
[2025-12-08 19:11:56] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:11:56] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:11:56] [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 19:12:01] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:01] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:01] [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 19:12:06] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:06] [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 19:12:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:07] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:07] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:07] [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 19:12:07] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:12:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2025-12-08 19:12:07] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:12:07] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:12:07] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 9.
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-9.html
[2025-12-08 19:12:07] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:07] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:07] [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 19:12:12] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:12] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:12] [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 19:12:17] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:17] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:17] [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 19:12:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:18] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:18] [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 19:12:18] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:12:18] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:19] [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 19:12:19] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:12:19] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:12:19] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 10.
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-10.html
[2025-12-08 19:12:19] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:19] [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 19:12:24] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:24] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:24] [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 19:12:29] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:29] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:29] [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 19:12:29] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:29] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:29] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:29] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:29] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:29] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:29] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:30] [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); 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 19:12:30] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from extra_attrs.Rmd:55-58 [load-interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:12:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2025-12-08 19:12:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:12:33] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:12:33] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 11.
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-11.html
[2025-12-08 19:12:33] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:33] [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 19:12:38] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:38] [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 19:12:43] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:43] [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 19:12:43] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:43] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:43] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:43] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:43] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:44] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:44] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:45] [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 19:12:45] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:12:46] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:12:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:12:47] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:12:47] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:12:48] [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 19:12:48] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:12:48] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:12:48] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 12.
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-12.html
[2025-12-08 19:12:48] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:48] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:48] [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 19:12:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:53] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:53] [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 19:12:58] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:12:58] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:12:58] [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 19:12:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:12:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:12:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:12:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:12:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:13:00] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:13:00] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:13:01] [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 19:13:01] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from omnipath_intro.Rmd:166-175 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 19:13:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2025-12-08 19:13:02] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-08 19:13:02] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:13:02] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 13.
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-13.html
[2025-12-08 19:13:02] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:13:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:03] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:03] [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 19:13:08] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:08] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:08] [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 19:13:13] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:13] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:13] [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 19:13:13] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:13:13] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:13:13] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:13:13] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:13:13] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:13:13] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:13:13] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:13:13] [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 19:13:13] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:13:14] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:13:14] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:13:14] [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 19:13:14] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 14.
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-14.html
[2025-12-08 19:13:14] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:14] [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 19:13:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:19] [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 19:13:24] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-12-08 19:13:24] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-12-08 19:13:24] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-08 19:13:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-08 19:13:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-12-08 19:13:25] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-12-08 19:13:25] [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 19:13:25] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-08 19:13:25] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08
[2025-12-08 19:13:25] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-12-09 00:10:16 UTC; unix
[2025-12-08 19:13:25] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-12-08 19:13:25] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-12-08 19:13:25] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-12-08 19:13:25] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-08 19:13:25] [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); 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 19:13:25] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

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