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This page was generated on 2026-02-23 11:57 -0500 (Mon, 23 Feb 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4890
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 888/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.6.0  (landing page)
Angelo Velle
Snapshot Date: 2026-02-22 13:45 -0500 (Sun, 22 Feb 2026)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: RELEASE_3_22
git_last_commit: d433a6d
git_last_commit_date: 2025-10-29 11:30:01 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
See other builds for gINTomics in R Universe.

BUILD results for gINTomics on nebbiolo2

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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: gINTomics
Version: 1.6.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gINTomics
StartedAt: 2026-02-22 17:59:11 -0500 (Sun, 22 Feb 2026)
EndedAt: 2026-02-22 18:09:02 -0500 (Sun, 22 Feb 2026)
EllapsedTime: 591.5 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 gINTomics
###
##############################################################################
##############################################################################


* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* preparing ‘gINTomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gINTomics.Rmd’ using rmarkdown
[2026-02-22 18:00:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:00:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-22 20:14:20 UTC; unix
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-22 18:00:47] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-22 18:00:47] [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=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-22 18:00:48] [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]
[2026-02-22 18:00:49] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2026-02-22); backports 1.5.0(2024-05-23); Biobase 2.70.0(2026-02-22); BiocBaseUtils 1.12.0(2026-02-22); BiocGenerics 0.56.0(2026-02-22); BiocIO 1.20.0(2026-02-22); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-22); BiocStyle 2.38.0(2026-02-22); Biostrings 2.78.0(2026-02-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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); cigarillo 1.0.0(2026-02-22); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.1(2026-02-22); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.36.0(2026-02-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.46.0(2026-02-22); GenomicFeatures 1.62.0(2026-02-22); GenomicRanges 1.62.1(2026-02-22); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.6.0(2026-02-22); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); 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); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.18.1(2026-02-22); IRanges 2.44.0(2026-02-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.50.0(2026-02-22); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2026-02-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2026-02-22); OmnipathR 3.18.4(2026-02-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); 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); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.26.0(2026-02-22); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.70.1(2026-02-22); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-22); S4Vectors 0.48.0(2026-02-22); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.0.0(2026-02-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.10.8(2026-02-22); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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); viridisLite 0.4.3(2026-02-04); 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); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-22); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-22 18:00:49] [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
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:00:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2026-02-22 18:01:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:13] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:13] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-22 18:01:13] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:01:13] [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]
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-22 18:01:13] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-22 18:01:14] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-22 18:01:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-22 18:01:14] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.698565s from rescued.omnipathdb.org (57.1 Kb/s); Redirect: 0s, DNS look up: 0.021854s, Connection: 0.022559s, Pretransfer: 0.353295s, First byte at: 0.494504s
[2026-02-22 18:01:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 22 Feb 2026 23:01:14 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: Mon, 23 Feb 2026 00:01:14 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-22 18:01:14] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sun, 22 Feb 2026 23:01:14 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=Mon, 23 Feb 2026 00:01:14 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-22 18:01:15] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:15] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-22 18:01:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:16] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-22 18:01:16] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] Downloaded 12.6 Kb in 0.424445s from omabrowser.org (29.7 Kb/s); Redirect: 0s, DNS look up: 0.185411s, Connection: 0.19848s, Pretransfer: 0.297274s, First byte at: 0.423801s
[2026-02-22 18:01:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sun, 22 Feb 2026 23:01:16 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=%2BzA2mLkECCjmrrdFHY5PXZElFDSnhQNl8Fk0Mpw%2FhrdiKzRlEabyvN5lRPmAvPMjGhvrAmSgitDV5CswDhJhoA2eunRxRLCUzzIxyUsv"}]}; cf-ray: 9d221ab9182b706a-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-22 18:01:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-22 18:01:18] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:18] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-22 18:01:18] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 18:01:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:01:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-22 18:04:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 18:04:03] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 13.070787s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00305s, Connection: 0.003895s, Pretransfer: 0.349879s, First byte at: 2m 13.070761s
[2026-02-22 18:04:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sun, 22 Feb 2026 23:04:03 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 18:04:03] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:04:03] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:04:08] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:04:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:04:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:04:08] [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]
[2026-02-22 18:06:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 18:06:22] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.173771s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.003988s, Connection: 0.004725s, Pretransfer: 0.373823s, First byte at: 2m 14.173733s
[2026-02-22 18:06:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sun, 22 Feb 2026 23:06:22 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 18:06:22] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:06:22] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:06:27] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:06:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:06:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:06:28] [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]
[2026-02-22 18:08:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 502.
[2026-02-22 18:08:42] [TRACE]   [OmnipathR] Downloaded 0 bytes in 2m 14.144123s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.018462s, Connection: 0.019283s, Pretransfer: 0.243246s, First byte at: 2m 14.144078s
[2026-02-22 18:08:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 502 Bad Gateway; Server: nginx; Date: Sun, 22 Feb 2026 23:08:42 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 150; Connection: keep-alive
[2026-02-22 18:08:42] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:08:42] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:08:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 18:08:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 18:08:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-22 20:14:20 UTC; unix
[2026-02-22 18:08:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-22 18:08:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-22 18:08:43] [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=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-22 18:08:43] [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]
[2026-02-22 18:08:44] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2026-02-22); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.70.0(2026-02-22); BiocBaseUtils 1.12.0(2026-02-22); BiocFileCache 3.0.0(2026-02-22); BiocGenerics 0.56.0(2026-02-22); BiocIO 1.20.0(2026-02-22); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-22); BiocStyle 2.38.0(2026-02-22); biomaRt 2.66.1(2026-02-22); Biostrings 2.78.0(2026-02-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.0.0(2026-02-22); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); clusterProfiler 4.18.4(2026-02-22); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.1(2026-02-22); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); dbplyr 2.5.2(2026-02-13); DelayedArray 0.36.0(2026-02-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); DOSE 4.4.0(2026-02-22); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); edgeR 4.8.2(2026-02-22); enrichplot 1.30.4(2026-02-22); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-02-22); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.5.0(2026-02-09); generics 0.1.4(2025-05-09); GenomicAlignments 1.46.0(2026-02-22); GenomicFeatures 1.62.0(2026-02-22); GenomicRanges 1.62.1(2026-02-22); GetoptLong 1.1.0(2025-11-28); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.6(2026-02-21); ggnewscale 0.5.2(2025-06-20); ggplot2 4.0.2(2026-02-03); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.1.1(2026-01-16); ggtree 4.0.4(2026-02-22); ggvenn 0.1.19(2025-10-08); gINTomics 1.6.0(2026-02-22); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-17); GOSemSim 2.36.0(2026-02-22); graph 1.88.1(2026-02-22); graphite 1.56.0(2026-02-22); graphlayouts 1.2.3(2026-02-21); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.18.1(2026-02-22); IRanges 2.44.0(2026-02-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.50.0(2026-02-22); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); limma 3.66.0(2026-02-22); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2026-02-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2026-02-22); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-22); org.Hs.eg.db 3.22.0(2025-11-17); org.Mm.eg.db 3.22.0(2025-11-17); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); 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 1.2.1(2026-01-09); qvalue 2.42.0(2026-02-22); 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); randomForest 4.7-1.2(2024-09-22); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); reactome.db 1.95.0(2026-01-15); ReactomePA 1.54.0(2026-02-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.26.0(2026-02-22); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.70.1(2026-02-22); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-22); S4Vectors 0.48.0(2026-02-22); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scatterpie 0.2.6(2025-09-12); selectr 0.5-1(2025-12-17); Seqinfo 1.0.0(2026-02-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); shiny.gosling 1.6.0(2026-02-22); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.1(2026-01-15); SparseArray 1.10.8(2026-02-22); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidydr 0.0.6(2025-07-25); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); tidytree 0.4.7(2026-01-08); timechange 0.4.0(2026-01-29); treeio 1.34.0(2026-02-22); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-17); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-17); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); visNetwork 2.1.4(2025-09-04); 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); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-22); yaml 2.3.12(2025-12-10); yulab.utils 0.2.4(2026-02-02); zip 2.3.3(2025-05-13)
[2026-02-22 18:08:44] [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
[2026-02-22 18:08:47] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`; error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 502
[2026-02-22 18:08:47] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 18:08:47] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 18:08:47] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-22 20:14:20 UTC; unix
[2026-02-22 18:08:47] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-22 18:08:47] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-22 18:08:47] [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=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-22 18:08:47] [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]
[2026-02-22 18:08:48] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2026-02-22); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.70.0(2026-02-22); BiocBaseUtils 1.12.0(2026-02-22); BiocFileCache 3.0.0(2026-02-22); BiocGenerics 0.56.0(2026-02-22); BiocIO 1.20.0(2026-02-22); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-22); BiocStyle 2.38.0(2026-02-22); biomaRt 2.66.1(2026-02-22); Biostrings 2.78.0(2026-02-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.0.0(2026-02-22); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); clusterProfiler 4.18.4(2026-02-22); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.1(2026-02-22); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); dbplyr 2.5.2(2026-02-13); DelayedArray 0.36.0(2026-02-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); DOSE 4.4.0(2026-02-22); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); edgeR 4.8.2(2026-02-22); enrichplot 1.30.4(2026-02-22); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-02-22); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.5.0(2026-02-09); generics 0.1.4(2025-05-09); GenomicAlignments 1.46.0(2026-02-22); GenomicFeatures 1.62.0(2026-02-22); GenomicRanges 1.62.1(2026-02-22); GetoptLong 1.1.0(2025-11-28); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.6(2026-02-21); ggnewscale 0.5.2(2025-06-20); ggplot2 4.0.2(2026-02-03); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.1.1(2026-01-16); ggtree 4.0.4(2026-02-22); ggvenn 0.1.19(2025-10-08); gINTomics 1.6.0(2026-02-22); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-17); GOSemSim 2.36.0(2026-02-22); graph 1.88.1(2026-02-22); graphite 1.56.0(2026-02-22); graphlayouts 1.2.3(2026-02-21); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.18.1(2026-02-22); IRanges 2.44.0(2026-02-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.50.0(2026-02-22); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); limma 3.66.0(2026-02-22); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2026-02-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2026-02-22); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-22); org.Hs.eg.db 3.22.0(2025-11-17); org.Mm.eg.db 3.22.0(2025-11-17); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); 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 1.2.1(2026-01-09); qvalue 2.42.0(2026-02-22); 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); randomForest 4.7-1.2(2024-09-22); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); reactome.db 1.95.0(2026-01-15); ReactomePA 1.54.0(2026-02-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.26.0(2026-02-22); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.70.1(2026-02-22); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-22); S4Vectors 0.48.0(2026-02-22); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scatterpie 0.2.6(2025-09-12); selectr 0.5-1(2025-12-17); Seqinfo 1.0.0(2026-02-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); shiny.gosling 1.6.0(2026-02-22); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.1(2026-01-15); SparseArray 1.10.8(2026-02-22); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidydr 0.0.6(2025-07-25); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); tidytree 0.4.7(2026-01-08); timechange 0.4.0(2026-01-29); treeio 1.34.0(2026-02-22); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-17); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-17); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); visNetwork 2.1.4(2025-09-04); 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); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-22); yaml 2.3.12(2025-12-10); yulab.utils 0.2.4(2026-02-02); zip 2.3.3(2025-05-13)
[2026-02-22 18:08:48] [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
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:08:48] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:08:48] [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]
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.310705s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.019408s, Connection: 0.020159s, Pretransfer: 0.0202s, First byte at: 0.310673s
[2026-02-22 18:08:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sun, 22 Feb 2026 23:08:48 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-22 18:08:48] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:48] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 1/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:53] [TRACE]   [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:08:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:08:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:08:53] [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]
[2026-02-22 18:08:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 18:08:54] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.28825s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00164s, Connection: 0.002374s, Pretransfer: 0.002414s, First byte at: 0.288215s
[2026-02-22 18:08:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sun, 22 Feb 2026 23:08:53 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-22 18:08:54] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:54] [WARN]    [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 2/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-22 18:08:59] [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]
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 500.
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] Downloaded 0 bytes in 0.28946s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.002123s, Connection: 0.00295s, Pretransfer: 0.003014s, First byte at: 0.289425s
[2026-02-22 18:08:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Sun, 22 Feb 2026 23:08:59 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-22 18:08:59] [WARN]    [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:59] [ERROR]   [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` (attempt 3/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:08:59] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 18:08:59] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 18:08:59] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-22 20:14:20 UTC; unix
[2026-02-22 18:08:59] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-22 18:08:59] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-22 18:08:59] [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=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-22 18:08:59] [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]
[2026-02-22 18:09:00] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2026-02-22); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.70.0(2026-02-22); BiocBaseUtils 1.12.0(2026-02-22); BiocFileCache 3.0.0(2026-02-22); BiocGenerics 0.56.0(2026-02-22); BiocIO 1.20.0(2026-02-22); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-22); BiocStyle 2.38.0(2026-02-22); biomaRt 2.66.1(2026-02-22); Biostrings 2.78.0(2026-02-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.0.0(2026-02-22); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); clusterProfiler 4.18.4(2026-02-22); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.1(2026-02-22); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); dbplyr 2.5.2(2026-02-13); DelayedArray 0.36.0(2026-02-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); DOSE 4.4.0(2026-02-22); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); edgeR 4.8.2(2026-02-22); enrichplot 1.30.4(2026-02-22); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-02-22); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.5.0(2026-02-09); generics 0.1.4(2025-05-09); GenomicAlignments 1.46.0(2026-02-22); GenomicFeatures 1.62.0(2026-02-22); GenomicRanges 1.62.1(2026-02-22); GetoptLong 1.1.0(2025-11-28); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.6(2026-02-21); ggnewscale 0.5.2(2025-06-20); ggplot2 4.0.2(2026-02-03); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.1.1(2026-01-16); ggtree 4.0.4(2026-02-22); ggvenn 0.1.19(2025-10-08); gINTomics 1.6.0(2026-02-22); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-17); GOSemSim 2.36.0(2026-02-22); graph 1.88.1(2026-02-22); graphite 1.56.0(2026-02-22); graphlayouts 1.2.3(2026-02-21); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.18.1(2026-02-22); IRanges 2.44.0(2026-02-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.50.0(2026-02-22); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); limma 3.66.0(2026-02-22); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2026-02-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2026-02-22); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-22); org.Hs.eg.db 3.22.0(2025-11-17); org.Mm.eg.db 3.22.0(2025-11-17); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); 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 1.2.1(2026-01-09); qvalue 2.42.0(2026-02-22); 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); randomForest 4.7-1.2(2024-09-22); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); reactome.db 1.95.0(2026-01-15); ReactomePA 1.54.0(2026-02-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.26.0(2026-02-22); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.70.1(2026-02-22); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-22); S4Vectors 0.48.0(2026-02-22); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scatterpie 0.2.6(2025-09-12); selectr 0.5-1(2025-12-17); Seqinfo 1.0.0(2026-02-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); shiny.gosling 1.6.0(2026-02-22); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.1(2026-01-15); SparseArray 1.10.8(2026-02-22); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidydr 0.0.6(2025-07-25); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); tidytree 0.4.7(2026-01-08); timechange 0.4.0(2026-01-29); treeio 1.34.0(2026-02-22); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-17); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-17); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); visNetwork 2.1.4(2025-09-04); 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); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-22); yaml 2.3.12(2025-12-10); yulab.utils 0.2.4(2026-02-02); zip 2.3.3(2025-05-13)
[2026-02-22 18:09:00] [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
[2026-02-22 18:09:01] [WARN]    [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`; error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic': The requested URL returned error: 500
[2026-02-22 18:09:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-22 18:09:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-02-22
[2026-02-22 18:09:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-22 20:14:20 UTC; unix
[2026-02-22 18:09:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-22 18:09:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-22 18:09:01] [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=2026-02-22; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-22 18:09:01] [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]
[2026-02-22 18:09:02] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2026-02-22); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.70.0(2026-02-22); BiocBaseUtils 1.12.0(2026-02-22); BiocFileCache 3.0.0(2026-02-22); BiocGenerics 0.56.0(2026-02-22); BiocIO 1.20.0(2026-02-22); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-22); BiocStyle 2.38.0(2026-02-22); biomaRt 2.66.1(2026-02-22); Biostrings 2.78.0(2026-02-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); 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); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.0.0(2026-02-22); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); clusterProfiler 4.18.4(2026-02-22); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.1(2026-02-22); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.2.3(2024-06-02); dbplyr 2.5.2(2026-02-13); DelayedArray 0.36.0(2026-02-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); DOSE 4.4.0(2026-02-22); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); edgeR 4.8.2(2026-02-22); enrichplot 1.30.4(2026-02-22); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-02-22); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.5.0(2026-02-09); generics 0.1.4(2025-05-09); GenomicAlignments 1.46.0(2026-02-22); GenomicFeatures 1.62.0(2026-02-22); GenomicRanges 1.62.1(2026-02-22); GetoptLong 1.1.0(2025-11-28); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.6(2026-02-21); ggnewscale 0.5.2(2025-06-20); ggplot2 4.0.2(2026-02-03); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.1.1(2026-01-16); ggtree 4.0.4(2026-02-22); ggvenn 0.1.19(2025-10-08); gINTomics 1.6.0(2026-02-22); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-17); GOSemSim 2.36.0(2026-02-22); graph 1.88.1(2026-02-22); graphite 1.56.0(2026-02-22); graphlayouts 1.2.3(2026-02-21); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.18.1(2026-02-22); IRanges 2.44.0(2026-02-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.50.0(2026-02-22); knitr 1.51(2025-12-20); later 1.4.6(2026-02-13); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); limma 3.66.0(2026-02-22); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2026-02-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2026-02-22); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-22); org.Hs.eg.db 3.22.0(2025-11-17); org.Mm.eg.db 3.22.0(2025-11-17); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); 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 1.2.1(2026-01-09); qvalue 2.42.0(2026-02-22); 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); randomForest 4.7-1.2(2024-09-22); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); reactome.db 1.95.0(2026-01-15); ReactomePA 1.54.0(2026-02-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.26.0(2026-02-22); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.70.1(2026-02-22); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-22); S4Vectors 0.48.0(2026-02-22); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scatterpie 0.2.6(2025-09-12); selectr 0.5-1(2025-12-17); Seqinfo 1.0.0(2026-02-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); shiny.gosling 1.6.0(2026-02-22); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.1(2026-01-15); SparseArray 1.10.8(2026-02-22); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidydr 0.0.6(2025-07-25); tidygraph 1.3.1(2024-01-30); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); tidytree 0.4.7(2026-01-08); timechange 0.4.0(2026-01-29); treeio 1.34.0(2026-02-22); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-17); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-17); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridis 0.6.5(2024-01-29); viridisLite 0.4.3(2026-02-04); visNetwork 2.1.4(2025-09-04); 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); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-22); yaml 2.3.12(2025-12-10); yulab.utils 0.2.4(2026-02-02); zip 2.3.3(2025-05-13)
[2026-02-22 18:09:02] [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
[2026-02-22 18:09:02] [SUCCESS] [OmnipathR] Downloaded 0 interactions.

Quitting from gINTomics.Rmd:138-142 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `tf_target[tf_target$source_genesymbol %in% genes, ]`:
! incorrect number of dimensions
---
Backtrace:
    ▆
 1. └─gINTomics::run_tf_integration(...)
 2.   └─gINTomics:::.def_tf_integration(...)
 3.     └─gINTomics:::.download_tf(genes = colnames(expression), species = species)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gINTomics.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘gINTomics.Rmd’

SUMMARY: processing the following file failed:
  ‘gINTomics.Rmd’

Error: Vignette re-building failed.
Execution halted