[ Started: 2026-11-01 19:17:18 CET ]
[ liana v0.1.14 for BioC-3.24 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ]
[ R version 4.6.1 Patched (2026-10-12 r90666) -- "Happy Hop" at /opt/R-4.6-patched/bin ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘liana’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘liana_cc2tensor.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-11-01 18:16:54 UTC; omnipath
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-11-01 18:16:56 UTC; unix
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.1.3
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Session info: [version=R version 4.6.1 Patched (2026-10-12 r90666); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-11-01; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-11-01 19:18:01] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; 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=/opt/R-4.6-patched/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-11-01 19:18:01] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.1(2026-04-03); basilisk 1.23.0(2026-11-01); Biobase 2.73.2(2026-07-29); BiocGenerics 0.59.12(2026-08-11); BiocManager 1.30.27(2025-11-14); BiocStyle 2.41.0(2026-04-28); bit 4.6.0(2025-03-06); bit64 4.8.6(2026-09-01); blob 1.3.0(2026-01-14); bookdown 0.48(2026-08-28); bslib 0.12.0(2026-08-04); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); circlize 0.4.18(2026-04-04); cli 3.6.6(2026-04-09); clue 0.3-68(2026-03-26); cluster 2.1.8.3(2026-07-30); codetools 0.2-20(2024-03-31); colorspace 2.1-4(2026-10-08); ComplexHeatmap 2.29.0(2026-04-28); crayon 1.5.3(2024-06-20); curl 8.1.0(2026-10-14); DBI 1.3.0(2026-02-25); DelayedArray 0.39.8(2026-09-30); digest 0.6.39(2025-11-19); dir.expiry 1.21.0(2026-04-28); doParallel 1.0.17(2022-02-07); dotCall64 1.2(2024-10-04); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); filelock 1.0.3(2023-12-11); forcats 1.0.1(2025-09-25); foreach 1.5.2(2022-02-02); fs 2.1.0(2026-04-18); future 1.80.0(2026-10-16); future.apply 1.21.0(2026-10-16); generics 0.1.4(2025-05-09); GenomicRanges 1.65.4(2026-09-02); GetoptLong 1.1.1(2026-04-08); ggplot2 4.0.3(2026-04-22); GlobalOptions 0.1.4(2026-04-08); globals 0.20.0(2026-10-11); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.9(2026-09-01); httr2 1.3.0(2026-07-13); igraph 2.3.4(2026-09-30); IRanges 2.47.5(2026-08-27); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.52(2026-09-06); later 1.4.8(2026-03-05); lattice 0.23-1(2026-08-12); liana 0.1.14(2026-11-01); lifecycle 1.0.5(2026-01-08); listenv 1.1.0(2026-10-04); logger 0.4.3(2026-08-24); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); Matrix 1.7-6(2026-07-25); MatrixGenerics 1.25.0(2026-04-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 4.1.3(2026-11-01); otel 0.2.0(2025-08-29); parallelly 1.50.0(2026-10-31); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 1.1.0(2026-10-18); purrr 1.2.2(2026-04-10); 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 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.6.0(2026-10-17); reticulate 1.47.0(2026-09-03); rjson 0.2.23(2024-09-16); rlang 1.3.0(2026-07-05); rmarkdown 2.32(2026-09-01); RSQLite 3.53.3(2026-06-30); rvest 1.0.5(2025-08-29); S4Arrays 1.13.2(2026-09-30); S4Vectors 0.51.10(2026-09-16); S7 0.2.2(2026-04-22); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.3.2(2026-08-27); sessioninfo 1.2.4(2026-06-04); SeuratObject 5.4.0(2026-04-11); shape 1.4.6.1(2024-02-23); SingleCellExperiment 1.35.2(2026-07-16); sp 2.2-4(2026-10-11); spam 2.11-4(2026-05-29); SparseArray 1.13.4(2026-09-30); stringi 1.8.9(2026-08-04); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.43.0(2026-04-28); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); tidyverse 2.0.0(2023-02-22); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.3(2026-06-19); xfun 0.62(2026-10-16); XML 3.99-0.25(2026-09-27); xml2 1.6.0(2026-06-22); XVector 0.53.0(2026-04-28); yaml 2.3.12(2025-12-10); zip 3.0.2(2026-08-04)
[2026-11-01 19:18:01] [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
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Contains 1 files.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:01] [TRACE]   [OmnipathR] Cache locked: FALSE

Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
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Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4]
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NULL
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Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
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Error: processing vignette 'liana_cc2tensor.Rmd' failed with diagnostics:
R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
--- failed re-building ‘liana_cc2tensor.Rmd’

--- re-building ‘liana_custom_op.Rmd’ using rmarkdown
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions]
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:18:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-11-01 19:18:20] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:20] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:20] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-11-01 19:18:20] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] No downlad stats available: no curl handle.
[2026-11-01 19:18:20] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sun, 01 Nov 2026 18:18:20 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=Sun, 01 Nov 2026 19:18:20 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-11-01 19:18:21] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:21] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-11-01 19:18:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-11-01 19:18:21] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] Downloaded 8.6 Kb in 0.280043s from omabrowser.org (30.8 Kb/s); Redirect: 0.100312s, DNS look up: 0.029076s, Connection: 0.047419s, Pretransfer: 0.137162s, First byte at: 0.278939s
[2026-11-01 19:18:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 302 ; date: Sun, 01 Nov 2026 18:18:21 GMT; content-type: text/html; charset=utf-8; location: https://zenodo.org/records/23757651/files/oma-species.txt?download=1; server: cloudflare; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; access-control-allow-origin: *; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; strict-transport-security: max-age=15768000; cf-cache-status: DYNAMIC; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=giyzR9D3WjZoPjpgnemKLl%2FAW2ZZBgf%2FUvTNGCUnpfgsD8A%2BrblTqB%2F9r1REVlhADmX%2BFnKw2m%2F1DxUmVv7%2BacF15NKqUrgMCXswhpnClzabRSw8k%2BQSZ4WSmN%2BqgWj6"}]}; cf-ray: a53ce6cb0dd4d243-FRA; HTTP/1.1 200 OK; server: nginx; date: Sun, 01 Nov 2026 18:18:21 GMT; content-type: text/plain; charset=utf-8; transfer-encoding: chunked; vary: Accept-Encoding; content-disposition: attachment; filename=oma-species.txt; set-cookie: session=ac7ea3accaf7afcf_6ae7826d.854Qz8VrRHxDjTYEwDPKcoHWMww; Expires=Fri, 06 Nov 2026 18:18:21 GMT; Secure; HttpOnly; Path=/; SameSite=Lax; oc-checksum: MD5:be0e147d873e195c8d84d3a7d485638; accept-ranges: bytes; content-type: text/plain; charset=utf-8; content-security-policy: default-src 'self' fonts.googleapis.com *.gstatic.com data: 'unsafe-inline' 'unsafe-eval' blob: zenodo-broker.web.cern.ch zenodo-broker-qa.web.cern.ch maxcdn.bootstrapcdn.com cdnjs.cloudflare.com ajax.googleapis.com webanalytics.web.cern.ch; x-content-type-options: nosniff; x-download-options: noopen; x-permitted-cross-domain-policies: none; x-frame-options: sameorigin; x-xss-protection: 1; mode=block; x-ratelimit-limit: 133; x-ratelimit-remaining: 132; x-ratelimit-reset: 1793557162; retry-after: 60; strict-transport-security: max-age=31556926; includeSubDomains; referrer-policy: strict-origin-when-cross-origin; x-source: files-primary; content-encoding: gzip
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:22] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-11-01 19:18:22] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:22] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-11-01 19:18:22] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-11-01 19:18:22] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-11-01 19:18:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:50] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-11-01 19:18:50] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:50] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/resources`
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omnipathdb.org/resources`.
[2026-11-01 19:18:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/resources`
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/resources`
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:51] [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]
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] Downloaded 4.8 Kb in 0.081577s from omnipathdb.org (59.3 Kb/s); Redirect: 0s, DNS look up: 0.001208s, Connection: 0.024102s, Pretransfer: 0.057155s, First byte at: 0.081435s
[2026-11-01 19:18:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:18:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:18:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Cache item `fd3330be7dde86b8e516b9b79adf4a3ebd50941b` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Download ready [key=fd3330be7dde86b8e516b9b79adf4a3ebd50941b, version=1]
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Cache item `fd3330be7dde86b8e516b9b79adf4a3ebd50941b` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097152s from omnipathdb.org (161.6 Kb/s); Redirect: 0s, DNS look up: 0.001028s, Connection: 0.022062s, Pretransfer: 0.05493s, First byte at: 0.096823s
[2026-11-01 19:18:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:18:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:18:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1]
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:54] [SUCCESS] [OmnipathR] Downloaded 5053 interactions.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions]
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.119642s from omnipathdb.org (131.2 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.023248s, Pretransfer: 0.074488s, First byte at: 0.119248s
[2026-11-01 19:18:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:18:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:18:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:18:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1]
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-11-01 19:18:56] [SUCCESS] [OmnipathR] Downloaded 3046 interactions.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions]
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105844s from omnipathdb.org (148.3 Kb/s); Redirect: 0s, DNS look up: 0.000982s, Connection: 0.024543s, Pretransfer: 0.057885s, First byte at: 0.105412s
[2026-11-01 19:18:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:18:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:18:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:18:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:57] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2026-11-01 19:18:57] [INFO]    [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1]
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:57] [INFO]    [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`.
[2026-11-01 19:18:57] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-11-01 19:18:58] [SUCCESS] [OmnipathR] Downloaded 3763 interactions.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions]
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.114313s from omnipathdb.org (137.3 Kb/s); Redirect: 0s, DNS look up: 0.001049s, Connection: 0.021877s, Pretransfer: 0.07157s, First byte at: 0.113339s
[2026-11-01 19:18:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:18:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:18:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:18:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:59] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2026-11-01 19:18:59] [INFO]    [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1]
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:18:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:18:59] [INFO]    [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-11-01 19:19:00] [SUCCESS] [OmnipathR] Downloaded 2483 interactions.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions]
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:00] [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]
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.117138s from omnipathdb.org (134 Kb/s); Redirect: 0s, DNS look up: 0.001044s, Connection: 0.023148s, Pretransfer: 0.072613s, First byte at: 0.116756s
[2026-11-01 19:19:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:00 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1]
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-11-01 19:19:02] [SUCCESS] [OmnipathR] Downloaded 3138 interactions.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions]
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=SignaLink3,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=SignaLink3,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101664s from omnipathdb.org (154.4 Kb/s); Redirect: 0s, DNS look up: 0.001097s, Connection: 0.023228s, Pretransfer: 0.056725s, First byte at: 0.101222s
[2026-11-01 19:19:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1]
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:04] [SUCCESS] [OmnipathR] Downloaded 1799 interactions.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations]
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/resources`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fd3330be7dde86b8e516b9b79adf4a3ebd50941b-1.rds`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.119381s from omnipathdb.org (131.5 Kb/s); Redirect: 0s, DNS look up: 0.001068s, Connection: 0.023219s, Pretransfer: 0.074678s, First byte at: 0.119024s
[2026-11-01 19:19:04] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic`
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:05] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`.
[2026-11-01 19:19:05] [INFO]    [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1]
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:05] [INFO]    [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:05] [SUCCESS] [OmnipathR] Downloaded 2076 annotation records.
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105418s from omnipathdb.org (148.9 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.021757s, Pretransfer: 0.063193s, First byte at: 0.104903s
[2026-11-01 19:19:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:19:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:09] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-11-01 19:19:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-11-01 19:19:11] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-11-01 19:19:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:11] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:11] [SUCCESS] [OmnipathR] Downloaded 395500 intercellular communication role records.
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.106927s from omnipathdb.org (146.8 Kb/s); Redirect: 0s, DNS look up: 0.000898s, Connection: 0.024893s, Pretransfer: 0.05794s, First byte at: 0.106287s
[2026-11-01 19:19:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:19:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:13] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-11-01 19:19:14] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:14] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:14] [SUCCESS] [OmnipathR] Downloaded 25476 intercellular communication role records.
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=datasets,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[datasets,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096292s from omnipathdb.org (163 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.021447s, Pretransfer: 0.054268s, First byte at: 0.095922s
[2026-11-01 19:19:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:16] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2026-11-01 19:19:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2026-11-01 19:19:17] [INFO]    [OmnipathR] Download ready [key=3098404926bc0cf155d043ff0c6efe64e3424b74, version=1]
[2026-11-01 19:19:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:17] [INFO]    [OmnipathR] Cache item `3098404926bc0cf155d043ff0c6efe64e3424b74` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:21] [SUCCESS] [OmnipathR] Downloaded 139851 interactions.
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=trans,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=trans,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.114026s from omnipathdb.org (137.7 Kb/s); Redirect: 0s, DNS look up: 0.001156s, Connection: 0.022982s, Pretransfer: 0.068376s, First byte at: 0.112863s
[2026-11-01 19:19:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:19:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:22] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2026-11-01 19:19:23] [INFO]    [OmnipathR] Download ready [key=1ac430724a20c137fc374a8499adabb468a12835, version=1]
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:23] [INFO]    [OmnipathR] Cache item `1ac430724a20c137fc374a8499adabb468a12835` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:23] [SUCCESS] [OmnipathR] Downloaded 42373 intercellular communication role records.
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=rec,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=rec,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Fallback URLs: `http://no-tls.omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:19:23] [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]
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.123895s from omnipathdb.org (126.7 Kb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.025279s, Pretransfer: 0.075078s, First byte at: 0.12332s
[2026-11-01 19:19:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:19:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sun, 01 Nov 2026 19:19:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-11-01 19:19:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:19:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:24] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:19:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2026-11-01 19:19:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2026-11-01 19:19:25] [INFO]    [OmnipathR] Download ready [key=552757063f9934c7b745a9c4247c3b5282a66c88, version=1]
[2026-11-01 19:19:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:19:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:19:25] [INFO]    [OmnipathR] Cache item `552757063f9934c7b745a9c4247c3b5282a66c88` version 1: status changed from `started` to `ready`.
[2026-11-01 19:19:25] [SUCCESS] [OmnipathR] Downloaded 50378 intercellular communication role records.
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:23:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-11-01 19:23:40] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic`
[2026-11-01 19:23:40] [SUCCESS] [OmnipathR] Loaded 395500 intercellular communication role records from cache.
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:23:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-11-01 19:23:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-11-01 19:23:41] [SUCCESS] [OmnipathR] Loaded 25476 intercellular communication role records from cache.
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=datasets,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[datasets,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:23:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`.
[2026-11-01 19:23:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic`
[2026-11-01 19:23:45] [SUCCESS] [OmnipathR] Loaded 139851 interactions from cache.
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=trans,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=trans,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`.
[2026-11-01 19:23:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic`
[2026-11-01 19:23:45] [SUCCESS] [OmnipathR] Loaded 42373 intercellular communication role records from cache.
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=rec,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=rec,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:23:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`.
[2026-11-01 19:23:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic`
[2026-11-01 19:23:45] [SUCCESS] [OmnipathR] Loaded 50378 intercellular communication role records from cache.

Quitting from liana_custom_op.Rmd:239-251 [liana_wrap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
     ▆
  1. ├─... %>% liana_aggregate()
  2. ├─liana::liana_aggregate(.)
  3. │ └─tibble::is_tibble(liana_res[[1]])
  4. └─liana::liana_wrap(testdata, resource = "custom", external_resource = pm_omni)
  5.   ├─liana::liana_prep(...)
  6.   └─liana:::liana_prep.Seurat(...)
  7.     ├─SingleCellExperiment::SingleCellExperiment(...)
  8.     │ └─SummarizedExperiment::SummarizedExperiment(...)
  9.     │   └─SummarizedExperiment:::normarg_assays(assays, as.null.if.no.assay = TRUE)
 10.     ├─SeuratObject::GetAssayData(object = sce, assay = assay, slot = "counts")
 11.     └─SeuratObject:::GetAssayData.Seurat(...)
 12.       └─SeuratObject::.Deprecate(...)
 13.         └─lifecycle::deprecate_stop(...)
 14.           └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics:
The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘liana_custom_op.Rmd’

--- re-building ‘liana_devel.Rmd’ using rmarkdown

Quitting from liana_devel.Rmd:41-52 [lr_cpdb]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
     ▆
  1. ├─liana::liana_prep(testdata)
  2. └─liana:::liana_prep.Seurat(testdata)
  3.   ├─SingleCellExperiment::SingleCellExperiment(...)
  4.   │ └─SummarizedExperiment::SummarizedExperiment(...)
  5.   │   └─SummarizedExperiment:::normarg_assays(assays, as.null.if.no.assay = TRUE)
  6.   ├─SeuratObject::GetAssayData(object = sce, assay = assay, slot = "counts")
  7.   └─SeuratObject:::GetAssayData.Seurat(...)
  8.     └─SeuratObject::.Deprecate(...)
  9.       └─lifecycle::deprecate_stop(...)
 10.         └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'liana_devel.Rmd' failed with diagnostics:
The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘liana_devel.Rmd’

--- re-building ‘liana_nichenet.Rmd’ using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Quitting from liana_nichenet.Rmd:91-99 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `Idents<-`:
! 'value' must be a factor or vector
---
Backtrace:
    ▆
 1. ├─SeuratObject::`Idents<-`(`*tmp*`, value = `<NULL>`)
 2. └─SeuratObject:::`Idents<-.Seurat`(`*tmp*`, value = `<NULL>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'liana_nichenet.Rmd' failed with diagnostics:
'value' must be a factor or vector
--- failed re-building ‘liana_nichenet.Rmd’

--- re-building ‘liana_ortho.Rmd’ using rmarkdown
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] Looking up in cache: `https://rescued.omnipathdb.org/homologene.data`.
[2026-11-01 19:31:29] [INFO]    [OmnipathR] Cache record does not exist: `https://rescued.omnipathdb.org/homologene.data`
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rescued.omnipathdb.org/homologene.data`.
[2026-11-01 19:31:29] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/homologene.data`
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/homologene.data`
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-11-01 19:31:29] [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]
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] Downloaded 31.7 Kb in 0.124306s from rescued.omnipathdb.org (254.7 Kb/s); Redirect: 0s, DNS look up: 0.018558s, Connection: 0.038562s, Pretransfer: 0.081687s, First byte at: 0.124208s
[2026-11-01 19:31:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 01 Nov 2026 18:31:29 GMT; Content-Type: application/octet-stream; Content-Length: 13803677; Last-Modified: Sat, 26 Nov 2022 19:03:22 GMT; Connection: keep-alive; ETag: "638262fa-d2a09d"; Expires: Sun, 01 Nov 2026 19:31:29 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY
[2026-11-01 19:31:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:31:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:31:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:31:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:31:32] [INFO]    [OmnipathR] Cache item `17adac3f05a1830fa9196b2637fd2121a4742cbb` version 1: status changed from `unknown` to `started`.
[2026-11-01 19:31:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17adac3f05a1830fa9196b2637fd2121a4742cbb-1.rds`.
[2026-11-01 19:31:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17adac3f05a1830fa9196b2637fd2121a4742cbb-1.rds`.
[2026-11-01 19:31:33] [INFO]    [OmnipathR] Download ready [key=17adac3f05a1830fa9196b2637fd2121a4742cbb, version=1]
[2026-11-01 19:31:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-11-01 19:31:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-11-01 19:31:33] [INFO]    [OmnipathR] Cache item `17adac3f05a1830fa9196b2637fd2121a4742cbb` version 1: status changed from `started` to `ready`.
[2026-11-01 19:31:33] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): downloaded 275237 records
[2026-11-01 19:31:34] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-11-01 19:31:34] [TRACE]   [OmnipathR] Looking up in cache: `https://rescued.omnipathdb.org/homologene.data`.
[2026-11-01 19:31:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/17adac3f05a1830fa9196b2637fd2121a4742cbb-1.rds`.
[2026-11-01 19:31:35] [SUCCESS] [OmnipathR] NCBI HomoloGene (rescued.omnipathdb.org): loaded 275237 records from cache

Quitting from liana_ortho.Rmd:78-104 [orthology]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/dplyr:::mutate_error>
Error in `mutate()`:
ℹ In argument: `across(all_of(columns), ~recode.character2(.x,
  .missing_fun = .missing_fun))`.
Caused by error in `across()`:
! Can't compute column `source_genesymbol`.
---
Backtrace:
     ▆
  1. ├─liana::generate_homologs(op_resource = op_resource, target_organism = 10090)
  2. │ └─op_notmany %>% left_join(op_resource, by = columns) %>% ...
  3. ├─liana:::.handle_complexes(...)
  4. │ └─op_resource_decomplex %>% ...
  5. ├─dplyr::mutate(...)
  6. ├─dplyr:::mutate.data.frame(...)
  7. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  8. │   ├─base::withCallingHandlers(...)
  9. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 10. │     ├─base::withCallingHandlers(...)
 11. │     └─mask$eval_all_mutate(quo)
 12. │       └─dplyr (local) eval()
 13. ├─liana:::recode.character2(source_genesymbol, .missing_fun = .missing_fun)
 14. │ └─dplyr:::find_template(values, .default, .missing)
 15. │   └─rlang::abort("No replacements provided.", call = error_call)
 16. │     └─rlang:::signal_abort(cnd, .file)
 17. │       └─base::signalCondition(cnd)
 18. └─dplyr (local) `<fn>`(`<rlng_rrr>`)
Caused by error in `recode.character2()`:
! No replacements provided.
---
Backtrace:
     ▆
  1. ├─liana::generate_homologs(op_resource = op_resource, target_organism = 10090)
  2. │ └─op_notmany %>% left_join(op_resource, by = columns) %>% ...
  3. ├─liana:::.handle_complexes(...)
  4. │ └─op_resource_decomplex %>% ...
  5. ├─dplyr::mutate(...)
  6. ├─dplyr:::mutate.data.frame(...)
  7. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  8. │   ├─base::withCallingHandlers(...)
  9. │   └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 10. │     ├─base::withCallingHandlers(...)
 11. │     └─mask$eval_all_mutate(quo)
 12. │       └─dplyr (local) eval()
 13. └─liana:::recode.character2(source_genesymbol, .missing_fun = .missing_fun)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'liana_ortho.Rmd' failed with diagnostics:
ℹ In argument: `across(all_of(columns), ~recode.character2(.x,
  .missing_fun = .missing_fun))`.
Caused by error in `across()`:
! Can't compute column `source_genesymbol`.
Caused by error in `recode.character2()`:
! No replacements provided.
--- failed re-building ‘liana_ortho.Rmd’

--- re-building ‘liana_tutorial.Rmd’ using rmarkdown

Quitting from liana_tutorial.Rmd:96-102 [liana_run]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
     ▆
  1. └─liana::liana_wrap(testdata)
  2.   ├─liana::liana_prep(...)
  3.   └─liana:::liana_prep.Seurat(...)
  4.     ├─SingleCellExperiment::SingleCellExperiment(...)
  5.     │ └─SummarizedExperiment::SummarizedExperiment(...)
  6.     │   └─SummarizedExperiment:::normarg_assays(assays, as.null.if.no.assay = TRUE)
  7.     ├─SeuratObject::GetAssayData(object = sce, assay = assay, slot = "counts")
  8.     └─SeuratObject:::GetAssayData.Seurat(...)
  9.       └─SeuratObject::.Deprecate(...)
 10.         └─lifecycle::deprecate_stop(...)
 11.           └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'liana_tutorial.Rmd' failed with diagnostics:
The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
--- failed re-building ‘liana_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘liana_cc2tensor.Rmd’ ‘liana_custom_op.Rmd’ ‘liana_devel.Rmd’
  ‘liana_nichenet.Rmd’ ‘liana_ortho.Rmd’ ‘liana_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2026-11-01 19:31:38 CET ]