[ Started: 2026-03-24 22:07:10 CET ] [ liana v0.1.14 for BioC-3.23 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ] * 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 '' [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-03-24 22:07:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-03-24 21:06:47 UTC; omnipath [2026-03-24 22:07:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-03-24 22:07:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-24 21:06:49 UTC; unix [2026-03-24 22:07:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.8 [2026-03-24 22:07:51] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-03-24 22:07:51] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); 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=2026-03-24; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-03-24 22:07:51] [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-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-24 22:07:51] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); basilisk 1.23.0(2026-03-24); Biobase 2.71.0(2025-10-30); BiocGenerics 0.57.0(2025-10-30); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-01-30); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2025-10-31); digest 0.6.39(2025-11-19); dir.expiry 1.19.0(2025-10-30); doParallel 1.0.17(2022-02-07); dotCall64 1.2(2024-10-04); dplyr 1.2.0(2026-02-03); 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 2.0.1(2026-03-24); future 1.70.0(2026-03-14); future.apply 1.20.2(2026-02-20); generics 0.1.4(2025-05-09); GenomicRanges 1.63.1(2025-12-08); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); GlobalOptions 0.1.3(2025-11-28); globals 0.19.1(2026-03-13); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); IRanges 2.45.0(2025-10-31); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); liana 0.1.14(2026-03-24); lifecycle 1.0.5(2026-01-08); listenv 0.10.1(2026-03-10); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.23.0(2025-10-30); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-24); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); 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 0.18.0(2025-11-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reticulate 1.45.0(2026-02-13); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2025-11-25); S4Vectors 0.49.0(2025-10-30); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-10-31); sessioninfo 1.2.3(2025-02-05); SeuratObject 5.3.0(2025-12-12); shape 1.4.6.1(2024-02-23); SingleCellExperiment 1.33.1(2026-03-10); sp 2.2-1(2026-02-13); spam 2.11-3(2026-01-08); SparseArray 1.11.11(2026-03-08); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-06); 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 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); XVector 0.51.0(2025-10-31); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-24 22:07:51] [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 [2026-03-24 22:07:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Contains 1 files. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-24 22:07:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:07:52] [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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Quitting from liana_cc2tensor.Rmd:122-137 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 [2026-03-24 22:08:08] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2026-03-24 22:08:08] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:08] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-03-24 22:08:08] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-03-24 22:08:08] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-03-24 22:08:08] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-03-24 22:08:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:08] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-03-24 22:08:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:08] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-03-24 22:08:08] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-03-24 22:08:08] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-24 22:08:08] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-03-24 22:08:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-03-24 22:08:08] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-03-24 22:08:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-24 22:08:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:08] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-03-24 22:08:08] [TRACE] [OmnipathR] Sending HTTP request. [2026-03-24 22:08:09] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-03-24 22:08:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:09] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.127743s from rescued.omnipathdb.org (312 Kb/s); Redirect: 0s, DNS look up: 0.003472s, Connection: 0.025541s, Pretransfer: 0.062739s, First byte at: 0.105946s [2026-03-24 22:08:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:09 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: Tue, 24 Mar 2026 22:08:09 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-03-24 22:08:09] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 24 Mar 2026 21:08:09 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=Tue, 24 Mar 2026 22:08:09 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-03-24 22:08:09] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-03-24 22:08:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:09] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-03-24 22:08:09] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-24 22:08:10] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-03-24 22:08:10] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 22:08:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-03-24 22:08:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-24 22:08:10] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 22:08:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-03-24 22:08:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:10] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-03-24 22:08:10] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.106587s from omabrowser.org (71 Kb/s); Redirect: 0s, DNS look up: 0.000559s, Connection: 0.007709s, Pretransfer: 0.052903s, First byte at: 0.106142s [2026-03-24 22:08:10] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 24 Mar 2026 21:08:10 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=5jYByDqZAm%2BVxghrTDMO2IxuOs%2FAtOPWryPhflwvE0Zb4jGXveyze3l3ssy3JH8cPHbbwj%2BiR9ML8bivJ19ip62LwboV2oxm2VGenw%3D%3D"}]}; cf-ray: 9e18a64b6c4a9b45-FRA; alt-svc: h3=":443"; ma=86400 [2026-03-24 22:08:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-03-24 22:08:10] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-03-24 22:08:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:11] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:11] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-03-24 22:08:11] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-24 22:08:11] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 22:08:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-03-24 22:08:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:11] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-24 22:08:11] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 22:08:11] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-03-24 22:08:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-03-24 22:08:38] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-03-24 22:08:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:38] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:38] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache. [2026-03-24 22:08:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:39] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-24 22:08:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`. [2026-03-24 22:08:39] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1] [2026-03-24 22:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:39] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:39] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-03-24 22:08:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:39] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:39] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [TRACE] [OmnipathR] Attempting `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` [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [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` [2026-03-24 22:08:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100313s from omnipathdb.org (156.5 Kb/s); Redirect: 0s, DNS look up: 0.000921s, Connection: 0.021416s, Pretransfer: 0.058182s, First byte at: 0.099905s [2026-03-24 22:08:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:40] [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` [2026-03-24 22:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:40] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2026-03-24 22:08:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2026-03-24 22:08:40] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1] [2026-03-24 22:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:40] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:40] [SUCCESS] [OmnipathR] Downloaded 5048 interactions. [2026-03-24 22:08:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2026-03-24 22:08:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:41] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellPhoneDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [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` [2026-03-24 22:08:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.128335s from omnipathdb.org (122.3 Kb/s); Redirect: 0s, DNS look up: 0.000972s, Connection: 0.022457s, Pretransfer: 0.084749s, First byte at: 0.127971s [2026-03-24 22:08:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:42] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2026-03-24 22:08:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2026-03-24 22:08:42] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1] [2026-03-24 22:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:42] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:42] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-24 22:08:42] [SUCCESS] [OmnipathR] Downloaded 3004 interactions. [2026-03-24 22:08:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2026-03-24 22:08:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:42] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=Cellinker,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [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` [2026-03-24 22:08:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.110265s from omnipathdb.org (142.4 Kb/s); Redirect: 0s, DNS look up: 0.000984s, Connection: 0.019512s, Pretransfer: 0.072582s, First byte at: 0.109921s [2026-03-24 22:08:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:43] [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` [2026-03-24 22:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:43] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2026-03-24 22:08:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2026-03-24 22:08:43] [INFO] [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1] [2026-03-24 22:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:43] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:43] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-24 22:08:43] [SUCCESS] [OmnipathR] Downloaded 3763 interactions. [2026-03-24 22:08:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2026-03-24 22:08:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:43] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:43] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:44] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=talklr,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088362s from omnipathdb.org (177.7 Kb/s); Redirect: 0s, DNS look up: 0.001003s, Connection: 0.017428s, Pretransfer: 0.055108s, First byte at: 0.088007s [2026-03-24 22:08:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:44] [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` [2026-03-24 22:08:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:44] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2026-03-24 22:08:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2026-03-24 22:08:44] [INFO] [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1] [2026-03-24 22:08:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:44] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:44] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-24 22:08:45] [SUCCESS] [OmnipathR] Downloaded 2483 interactions. [2026-03-24 22:08:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2026-03-24 22:08:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:45] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:45] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:45] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CellChatDB,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [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` [2026-03-24 22:08:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108063s from omnipathdb.org (145.3 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.020742s, Pretransfer: 0.068166s, First byte at: 0.107709s [2026-03-24 22:08:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:46] [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` [2026-03-24 22:08:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:46] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2026-03-24 22:08:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2026-03-24 22:08:46] [INFO] [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1] [2026-03-24 22:08:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:46] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:46] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-03-24 22:08:46] [SUCCESS] [OmnipathR] Downloaded 3138 interactions. [2026-03-24 22:08:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions] [2026-03-24 22:08:46] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=SignaLink3,datasets=omnipath,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:46] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:47] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=SignaLink3,datasets=omnipath,types=,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:47] [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` [2026-03-24 22:08:47] [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` [2026-03-24 22:08:47] [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` [2026-03-24 22:08:47] [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` [2026-03-24 22:08:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-24 22:08:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-24 22:08:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-24 22:08:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.107061s from omnipathdb.org (146.6 Kb/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.018602s, Pretransfer: 0.071568s, First byte at: 0.106764s [2026-03-24 22:08:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-03-24 22:08:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:48] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-03-24 22:08:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2026-03-24 22:08:48] [INFO] [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1] [2026-03-24 22:08:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:48] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:48] [SUCCESS] [OmnipathR] Downloaded 1799 interactions. [2026-03-24 22:08:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-03-24 22:08:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations] [2026-03-24 22:08:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_function,datasets=,types=,genesymbols=yes,fields=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE] [2026-03-24 22:08:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-03-24 22:08:48] [TRACE] [OmnipathR] Orthology targets: [2026-03-24 22:08:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-03-24 22:08:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:48] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_function,datasets=,types=,default_fields=TRUE,silent=FALSE,logicals=,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=,exclude=,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)] [2026-03-24 22:08:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-03-24 22:08:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-03-24 22:08:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-03-24 22:08:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-03-24 22:08:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.114432s from omnipathdb.org (137.2 Kb/s); Redirect: 0s, DNS look up: 0.000977s, Connection: 0.021891s, Pretransfer: 0.07215s, First byte at: 0.11407s [2026-03-24 22:08:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 24 Mar 2026 21:08:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 24 Mar 2026 22:08:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-03-24 22:08:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2026-03-24 22:08:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:49] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`. [2026-03-24 22:08:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2026-03-24 22:08:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2026-03-24 22:08:49] [INFO] [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1] [2026-03-24 22:08:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-24 22:08:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-24 22:08:49] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`. [2026-03-24 22:08:49] [SUCCESS] [OmnipathR] Downloaded 2076 annotation records. [2026-03-24 22:08:49] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::filter_intercell_network(., simplify = FALSE, ...)`. [2026-03-24 22:08:49] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. Quitting from liana_custom_op.Rmd:158-196 [pm_omni] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `UseMethod()`: ! no applicable method for 'tbl_vars' applied to an object of class "NULL" --- Backtrace: ▆ 1. ├─liana::generate_omni(...) 2. │ └─... %>% ... 3. └─dplyr::distinct_at(...) 4. └─dplyr:::manip_at(...) 5. └─dplyr:::tbl_at_syms(...) 6. └─dplyr:::tbl_at_vars(...) 7. └─dplyr::tbl_vars(tbl) 8. ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x)) 9. │ └─base::structure(...) 10. └─dplyr:::tbl_vars_dispatch(x) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics: no applicable method for 'tbl_vars' applied to an object of class "NULL" --- failed re-building ‘liana_custom_op.Rmd’ --- re-building ‘liana_devel.Rmd’ using rmarkdown Quitting from liana_devel.Rmd:41-52 [lr_cpdb] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `Idents<-`: ! 'value' must be a factor or vector --- Backtrace: ▆ 1. ├─SeuratObject::`Idents<-`(`*tmp*`, value = ``) 2. └─SeuratObject:::`Idents<-.Seurat`(`*tmp*`, value = ``) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 [2026-03-24 22:11:47] [TRACE] [OmnipathR] Bypassing call: `homologene_raw()`. [2026-03-24 22:11:47] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. Quitting from liana_ortho.Rmd:72-74 [show_taxid] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `h()`: ! error in evaluating the argument 'object' in selecting a method for function 'na.omit': no applicable method for 'pull' applied to an object of class "list" --- Backtrace: ▆ 1. ├─liana::show_homologene() 2. │ └─... %>% print(n = nrow(.)) 3. ├─base::print(., n = nrow(.)) 4. ├─dplyr::arrange(., name) 5. ├─stats::na.omit(.) 6. ├─tibble::tibble(ncbi_taxid = ., name = common_name(.), latin = latin_name(.)) 7. │ └─tibble:::tibble_quos(xs, .rows, .name_repair) 8. │ └─rlang::eval_tidy(xs[[j]], mask) 9. ├─base::unique(.) 10. ├─dplyr::pull(., ncbi_taxid) 11. └─base::.handleSimpleError(...) 12. └─base (local) h(simpleError(msg, call)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_ortho.Rmd' failed with diagnostics: error in evaluating the argument 'object' in selecting a method for function 'na.omit': no applicable method for 'pull' applied to an object of class "list" --- failed re-building ‘liana_ortho.Rmd’ --- re-building ‘liana_tutorial.Rmd’ using rmarkdown Quitting from liana_tutorial.Rmd:96-102 [liana_run] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: 2026-03-24 22:11:49 CET ]