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This page was generated on 2026-02-21 11:32 -0500 (Sat, 21 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" 4871
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1505/2354HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.19.6  (landing page)
Denes Turei
Snapshot Date: 2026-02-20 13:40 -0500 (Fri, 20 Feb 2026)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 4c56371
git_last_commit_date: 2026-01-29 10:23:53 -0500 (Thu, 29 Jan 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for OmnipathR in R Universe.

BUILD results for OmnipathR on nebbiolo1

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: 3.19.6
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2026-02-20 19:09:31 -0500 (Fri, 20 Feb 2026)
EndedAt: 2026-02-20 19:17:41 -0500 (Fri, 20 Feb 2026)
EllapsedTime: 489.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-02-20 19:09:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-20
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-21 00:09:33 UTC; unix
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-20 19:09:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); 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=2026-02-20; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-20 19:09:57] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2026-02-20); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-20); 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 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-20 19:09:57] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp0ZtsLy/Rinst28476b107bcaa2/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp0ZtsLy/Rinst28476b107bcaa2/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp0ZtsLy/Rinst28476b107bcaa2/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/tmp/Rtmp0ZtsLy/Rinst28476b107bcaa2/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-20 19:09:57] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:09:57] [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]
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-02-20 19:09:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.638912s from rescued.omnipathdb.org (62.4 Kb/s); Redirect: 0s, DNS look up: 0.031177s, Connection: 0.031779s, Pretransfer: 0.34009s, First byte at: 0.490922s
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 21 Feb 2026 00:09:58 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 21 Feb 2026 01:09:58 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 21 Feb 2026 00:09:58 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 21 Feb 2026 01:09:58 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-20 19:09:58] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:58] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-20 19:09:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:09:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:09:59] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-20 19:09:59] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:09:59] [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]
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.409066s from omabrowser.org (18.5 Kb/s); Redirect: 0s, DNS look up: 0.026097s, Connection: 0.039022s, Pretransfer: 0.077673s, First byte at: 0.408605s
[2026-02-20 19:09:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 21 Feb 2026 00:09:59 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=r92XYmCAhaUoQQ6Z1RV8P2yG%2Ffwp23ErwS6IRoTQp5IRIzfZyH9XK2jLGlYJAUaoBJLhYZLQY4Yizm5nw8VnErr8qKHwOKxDwsPmZkVY"}]}; cf-ray: 9d1204a09d16c950-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-20 19:10:00] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:00] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-20 19:10:00] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:00] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-20 19:10:00] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-20 19:10:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-20 19:10:30] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:30] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:30] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-20 19:10:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:10:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-20 19:12:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-20 19:12:46] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.91532s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.004078s, Connection: 0.004789s, Pretransfer: 0.299904s, First byte at: 2m 14.91526s
[2026-02-20 19:12:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sat, 21 Feb 2026 00:12:46 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-20 19:12:46] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:12:46] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:12:51] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:12:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:12:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:12:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-20 19:15:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-20 19:15:05] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 13.993773s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.004258s, Connection: 0.00532s, Pretransfer: 0.319964s, First byte at: 2m 13.993716s
[2026-02-20 19:15:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sat, 21 Feb 2026 00:15:05 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-20 19:15:05] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:15:05] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:15:10] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:15:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:15:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:15:10] [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]
[2026-02-20 19:17:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-20 19:17:24] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.1548s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001883s, Connection: 0.002756s, Pretransfer: 0.310839s, First byte at: 2m 14.154741s
[2026-02-20 19:17:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sat, 21 Feb 2026 00:17:24 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-20 19:17:24] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:17:24] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:17:24] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-20 19:17:24] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-20
[2026-02-20 19:17:24] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-21 00:09:33 UTC; unix
[2026-02-20 19:17:24] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-20 19:17:24] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-20 19:17:26] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); 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=2026-02-20; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-20 19:17:26] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-20 19:17:26] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2026-02-20); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-20); 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 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-20 19:17:26] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-20 19:17:27] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`; error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 502
[2026-02-20 19:17:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-20 19:17:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-20
[2026-02-20 19:17:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-21 00:09:33 UTC; unix
[2026-02-20 19:17:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-20 19:17:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-20 19:17:29] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); 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=2026-02-20; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-20 19:17:29] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; 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-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-20 19:17:29] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2026-02-20); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); 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 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-20); 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 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-20 19:17:29] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:17:29] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:17:29] [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]
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.329676s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.006327s, Connection: 0.007212s, Pretransfer: 0.007307s, First byte at: 0.32962s
[2026-02-20 19:17:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 21 Feb 2026 00:17:29 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa5.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-20 19:17:29] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-20 19:17:29] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-20 19:17:34] [TRACE]   [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:17:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:17:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:17:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-20 19:17:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-20 19:17:35] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.300471s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.002332s, Connection: 0.003386s, Pretransfer: 0.003484s, First byte at: 0.300428s
[2026-02-20 19:17:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 21 Feb 2026 00:17:35 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa5.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-20 19:17:35] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-20 19:17:35] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.300819s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001478s, Connection: 0.00222s, Pretransfer: 0.002297s, First byte at: 0.300782s
[2026-02-20 19:17:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sat, 21 Feb 2026 00:17:40 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa5.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
[2026-02-20 19:17:40] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500

 *** caught segfault ***
address 0x100000012, cause 'memory not mapped'
*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
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*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
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*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation
*** recursive gc invocation

Traceback:
 1: as.list.default(sys.call())
 2: as.list(sys.call())
 3: alist(format)
 4: eval(substitute(alist(...)))
 5: eval(substitute(alist(...)))
 6: glue_data(.x = NULL, ..., .sep = .sep, .envir = .envir, .open = .open,     .close = .close, .na = .na, .null = .null, .comment = .comment,     .literal = .literal, .transformer = .transformer, .trim = .trim)
 7: glue::glue(format, .envir = meta)
 8: layout(level, res$message, namespace = namespace, .logcall = substitute(.logcall),     .topcall = substitute(.topcall), .topenv = .topenv, .timestamp = .timestamp)
 9: (function (level, ..., namespace = NA_character_, .logcall = sys.call(),     .topcall = sys.call(-1), .topenv = parent.frame(), .timestamp = Sys.time()) {    res <- list(level = level, namespace = namespace, params = list(...),         handlers = list(formatter = formatter, layout = layout,             appender = appender), message = NULL, record = NULL)    if (level > threshold) {        return(invisible(res))    }    if (length(res$params) == 1 && isTRUE(attr(res$params[[1]],         "skip_formatter", exact = TRUE))) {        res$message <- res$params[[1]]    }    else {        res$message <- do.call(formatter, c(res$params, list(.logcall = substitute(.logcall),             .topcall = substitute(.topcall), .topenv = .topenv)))    }    if (".timestamp" %in% names(formals(layout))) {        res$record <- layout(level, res$message, namespace = namespace,             .logcall = substitute(.logcall), .topcall = substitute(.topcall),             .topenv = .topenv, .timestamp = .timestamp)    }    else {        res$record <- layout(level, res$message, namespace = namespace,             .logcall = substitute(.logcall), .topcall = substitute(.topcall),             .topenv = .topenv)    }    appender(res$record)    invisible(res)})("HTTP request failed with error: %s", "Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500",     level = 300L, .logcall = log_warn("HTTP request failed with error: %s",         msg), .topcall = (function (url, curlopt = list(), callback = NULL,         compr = NULL, ...)     {        log_trace("HTTP request by `omnipath_curl`.")        handle <- exec(omnipath_new_handle, !!!curlopt)        compr %<>% get_compr(url, .)        if (!is.null(compr)) {            path <- url %>% fname_from_url %>% file.path(tempdir(),                 .)            log_trace(paste0("`%s` compressed file, downloading to ",                 "temporary location: `%s`"), compr, path)            curl_call <- quote(curl_fetch_disk(url, path, handle = handle))        }        else {            curl_call <- quote(curl(url, open = "rb", handle = handle))        }        con <- tryCatch(eval(curl_call), error = identity, warning = identity)        log_curl_stats(handle, url)        if (inherits(con, "condition")) {            msg <- conditionMessage(con)            log_warn("HTTP request failed with error: %s", msg)            stop(msg)        }        if (!is.null(compr)) {            con <- path %>% decompr(compr)        }        if (!is.null(callback)) {            result <- tryCatch({                callback(con, ...)            }, error = function(e) {                stop(e)            }, finally = {                close(con)            })            return(result)        }        return(con)    })("http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic",         curlopt = list(), callback = function (file, delim = NULL,             quote = "\"", escape_backslash = FALSE, escape_double = TRUE,             col_names = TRUE, col_types = NULL, col_select = NULL,             id = NULL, locale = default_locale(), na = c("",                 "NA"), quoted_na = deprecated(), comment = "",             trim_ws = FALSE, skip = 0, n_max = Inf, guess_max = min(1000,                 n_max), name_repair = "unique", num_threads = readr_threads(),             progress = show_progress(), show_col_types = should_show_types(),             skip_empty_rows = TRUE, lazy = should_read_lazy())         {            if (!is.null(delim) && !nzchar(delim)) {                stop("`delim` must be at least one character, ",                   "use `read_table()` for whitespace delimited input.",                   call. = FALSE)            }            if (edition_first()) {                quoted_na <- if (is_present(quoted_na)) {                  quoted_na                }                else {                  TRUE                }                tokenizer <- tokenizer_delim(delim, quote = quote,                   escape_backslash = escape_backslash, escape_double = escape_double,                   na = na, quoted_na = quoted_na, comment = comment,                   trim_ws = trim_ws, skip_empty_rows = skip_empty_rows)                return(read_delimited(file, tokenizer, col_names = col_names,                   col_types = col_types, locale = locale, skip = skip,                   skip_empty_rows = skip_empty_rows, comment = comment,                   n_max = n_max, guess_max = guess_max, progress = progress,                   show_col_types = show_col_types))            }            if (!missing(quoted_na)) {                lifecycle::deprecate_stop(when = "2.0.0", what = "readr::read_delim(quoted_na = )",                   details = c(i = "This argument is not supported in readr edition 2.",                     i = "Use `with_edition(1, ...)` or `local_edition(1)` to use the legacy edition 1."))            }            file <- standardise_literal_data(file, "read_delim",                 env = current_env(), user_env = caller_env())            vroom::vroom(file, delim = delim, col_names = col_names,                 col_types = col_types, col_select = {                  {                    col_select                  }                }, id = id, .name_repair = name_repair, skip = skip,                 n_max = n_max, na = na, quote = quote, comment = comment,                 skip_empty_rows = skip_empty_rows, trim_ws = trim_ws,                 escape_double = escape_double, escape_backslash = escape_backslash,                 locale = locale, guess_max = guess_max, progress = progress,                 altrep = lazy, show_col_types = show_col_types,                 num_threads = num_threads)        }, col_types = list(cols = list(dorothea_level = list()),             default = list(), delim = NULL), progress = FALSE,         show_col_types = FALSE, delim = "\t"), .topenv = <environment>,     .timestamp = 1771633060.70302, namespace = "OmnipathR")
10: do.call(log_fun, log_arg)
11: structure(do.call(log_fun, log_arg), class = "logger")
12: FUN(X[[i]], ...)
13: lapply(definitions, function(definition) {    if (level > definition$threshold) {        return(NULL)    }    log_fun <- do.call(logger, definition)    structure(do.call(log_fun, log_arg), class = "logger")})
14: log_level(WARN, ..., namespace = namespace, .logcall = .logcall,     .topcall = .topcall, .topenv = .topenv, .timestamp = .timestamp)
15: log_warn("HTTP request failed with error: %s", msg)
16: (function (url, curlopt = list(), callback = NULL, compr = NULL,     ...) {    log_trace("HTTP request by `omnipath_curl`.")    handle <- exec(omnipath_new_handle, !!!curlopt)    compr %<>% get_compr(url, .)    if (!is.null(compr)) {        path <- url %>% fname_from_url %>% file.path(tempdir(),             .)        log_trace(paste0("`%s` compressed file, downloading to ",             "temporary location: `%s`"), compr, path)        curl_call <- quote(curl_fetch_disk(url, path, handle = handle))    }    else {        curl_call <- quote(curl(url, open = "rb", handle = handle))    }    con <- tryCatch(eval(curl_call), error = identity, warning = identity)    log_curl_stats(handle, url)    if (inherits(con, "condition")) {        msg <- conditionMessage(con)        log_warn("HTTP request failed with error: %s", msg)        stop(msg)    }    if (!is.null(compr)) {        con <- path %>% decompr(compr)    }    if (!is.null(callback)) {        result <- tryCatch({            callback(con, ...)        }, error = function(e) {            stop(e)        }, finally = {            close(con)        })        return(result)    }    return(con)})("http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic",     curlopt = list(), callback = function (file, delim = NULL,         quote = "\"", escape_backslash = FALSE, escape_double = TRUE,         col_names = TRUE, col_types = NULL, col_select = NULL,         id = NULL, locale = default_locale(), na = c("", "NA"),         quoted_na = deprecated(), comment = "", trim_ws = FALSE,         skip = 0, n_max = Inf, guess_max = min(1000, n_max),         name_repair = "unique", num_threads = readr_threads(),         progress = show_progress(), show_col_types = should_show_types(),         skip_empty_rows = TRUE, lazy = should_read_lazy())     {        if (!is.null(delim) && !nzchar(delim)) {            stop("`delim` must be at least one character, ",                 "use `read_table()` for whitespace delimited input.",                 call. = FALSE)        }        if (edition_first()) {            quoted_na <- if (is_present(quoted_na)) {                quoted_na            }            else {                TRUE            }            tokenizer <- tokenizer_delim(delim, quote = quote,                 escape_backslash = escape_backslash, escape_double = escape_double,                 na = na, quoted_na = quoted_na, comment = comment,                 trim_ws = trim_ws, skip_empty_rows = skip_empty_rows)            return(read_delimited(file, tokenizer, col_names = col_names,                 col_types = col_types, locale = locale, skip = skip,                 skip_empty_rows = skip_empty_rows, comment = comment,                 n_max = n_max, guess_max = guess_max, progress = progress,                 show_col_types = show_col_types))        }        if (!missing(quoted_na)) {            lifecycle::deprecate_stop(when = "2.0.0", what = "readr::read_delim(quoted_na = )",                 details = c(i = "This argument is not supported in readr edition 2.",                   i = "Use `with_edition(1, ...)` or `local_edition(1)` to use the legacy edition 1."))        }        file <- standardise_literal_data(file, "read_delim",             env = current_env(), user_env = caller_env())        vroom::vroom(file, delim = delim, col_names = col_names,             col_types = col_types, col_select = {                {                  col_select                }            }, id = id, .name_repair = name_repair, skip = skip,             n_max = n_max, na = na, quote = quote, comment = comment,             skip_empty_rows = skip_empty_rows, trim_ws = trim_ws,             escape_double = escape_double, escape_backslash = escape_backslash,             locale = locale, guess_max = guess_max, progress = progress,             altrep = lazy, show_col_types = show_col_types, num_threads = num_threads)    }, col_types = list(cols = list(dorothea_level = list()),         default = list(), delim = NULL), progress = FALSE, show_col_types = FALSE,     delim = "\t")
17: exec(omnipath_curl, url, curlopt = curlopt, callback = read_delim,     !!!args)
18: (function (url, curlopt = list(), ...) {    args <- list(...) %>% add_defaults(read_delim, READR_DEFAULTS)    exec(omnipath_curl, url, curlopt = curlopt, callback = read_delim,         !!!args)})("http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic",     col_types = list(cols = list(dorothea_level = list()), default = list(),         delim = NULL), progress = FALSE, show_col_types = FALSE)
19: exec(fun, url, !!!args)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch(exec(fun, url, !!!args), error = identity)
24: download_base(the_url, fun, ...)
25: doTryCatch(return(expr), name, parentenv, handler)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
27: tryCatchList(expr, classes, parentenv, handlers)
28: tryCatch(download_base(the_url, fun, ...), error = function(e) {    log_warn("Failed to download: `%s`; error: %s", the_url,         conditionMessage(e))    nothing <- log_all_info("OmnipathR")    NULL})
29: (function (url, fun, cache = NULL, ...) {    cache %<>% use_cache    if (cache) {        for (the_url in url) {            log_trace("Looking up in cache: `%s`", the_url)            from_cache <- omnipath_cache_load(url = the_url)            if (!is.null(from_cache)) {                log_info("Loaded from cache: `%s`", the_url)                attr(from_cache, "url") <- the_url                return(from_cache)            }        }    }    for (the_url in url) {        log_trace("Attempting `%s`", the_url)        result <- tryCatch(download_base(the_url, fun, ...),             error = function(e) {                log_warn("Failed to download: `%s`; error: %s",                   the_url, conditionMessage(e))                nothing <- log_all_info("OmnipathR")                NULL            })        if (!is.null(result)) {            log_info("Successfully retrieved: `%s`", the_url)            if (cache) {                omnipath_cache_save(data = result, url = the_url)            }            attr(result, "url") <- the_url            return(result)        }    }})(url = c("https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic", "http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic"), cache = TRUE, fun = function (url, curlopt = list(), ...) {    args <- list(...) %>% add_defaults(read_delim, READR_DEFAULTS)    exec(omnipath_curl, url, curlopt = curlopt, callback = read_delim,         !!!args)}, col_types = list(cols = list(dorothea_level = list()), default = list(),     delim = NULL), progress = FALSE, show_col_types = FALSE)
30: do.call(omnipath_download, download_args)
31: omnipath_check_result(result, url)
32: omnipath_post_download(., url = url, logicals = logicals, references_by_resource = references_by_resource,     strict_evidences = strict_evidences, exclude = exclude, param = param,     add_counts = add_counts, silent = silent)
33: do.call(omnipath_download, download_args) %>% omnipath_post_download(url = url,     logicals = logicals, references_by_resource = references_by_resource,     strict_evidences = strict_evidences, exclude = exclude, param = param,     add_counts = add_counts, silent = silent)
34: (function (query_type, organism = 9606L, resources = NULL, datasets = NULL,     types = NULL, genesymbols = "yes", fields = NULL, default_fields = TRUE,     silent = FALSE, logicals = NULL, download_args = list(),     format = "data.frame", references_by_resource = TRUE, add_counts = TRUE,     license = NULL, password = NULL, exclude = NULL, json_param = list(),     strict_evidences = FALSE, genesymbol_resource = "UniProt",     cache = NULL, ...) {    datasets %<>% setdiff(exclude)    resources %<>% setdiff(exclude)    cache %<>% use_cache    param <- environment() %>% as.list %>% c(list(...)) %>% omnipath_check_param    url <- param %>% omnipath_build_url %>% c(if (getOption("omnipathr.notls_fallback") &&         !getOption("omnipathr.notls_force")) omnipath_build_url(param,         notls = TRUE) else NULL)    download_args_defaults <- list(url = url, cache = cache)    dataframe_defaults <- list(fun = curl_read_tsv, col_types = if ("dorothea_level" %in%         param$fields) cols(dorothea_level = col_character()) else cols(),         progress = FALSE, show_col_types = FALSE)    json_defaults <- list(fun = curl_read_json, simplifyDataFrame = FALSE)    download_args %<>% modifyList(if (empty_or_equals(param$format,         "json"))         json_defaults    else dataframe_defaults, .) %>% modifyList(download_args_defaults,         .)    result <- do.call(omnipath_download, download_args) %>% omnipath_post_download(url = url,         logicals = logicals, references_by_resource = references_by_resource,         strict_evidences = strict_evidences, exclude = exclude,         param = param, add_counts = add_counts, silent = silent)    return(result)})(dorothea_levels = c("A", "B"), query_type = "interactions",     datasets = c("dorothea", "tf_target", "collectri"))
35: exec(omnipath_query, !!!args)
36: transcriptional()
37: eval(expr, envir)
38: eval(expr, envir)
39: withVisible(eval(expr, envir))
40: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
41: eval(call)
42: eval(call)
43: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
44: doWithOneRestart(return(expr), restart)
45: withOneRestart(expr, restarts[[1L]])
46: withRestartList(expr, restarts[-nr])
47: doWithOneRestart(return(expr), restart)
48: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
49: withRestartList(expr, restarts)
50: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
51: evaluate::evaluate(...)
52: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
53: in_dir(input_dir(), expr)
54: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,     keep_message = if (is.numeric(options$message)) TRUE else options$message,     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
55: eng_r(options)
56: block_exec(params)
57: call_block(x)
58: process_group(group)
59: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
60: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
61: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
62: process_file(text, output)
63: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
64: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
65: vweave_rmarkdown(...)
66: engine$weave(file, quiet = quiet, encoding = enc)
67: doTryCatch(return(expr), name, parentenv, handler)
68: tryCatchOne(expr, names, parentenv, handlers[[1L]])
69: tryCatchList(expr, classes, parentenv, handlers)
70: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    output <- find_vignette_product(name, by = "weave", engine = engine)    if (!have.makefile && vignette_is_tex(output)) {        texi2pdf(file = output, clean = FALSE, quiet = quiet)        output <- find_vignette_product(name, by = "texi2pdf",             engine = engine)    }    outputs <- c(outputs, output)}, error = function(e) {    thisOK <<- FALSE    fails <<- c(fails, file)    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
71: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)