[ Started: 2026-10-20 19:17:26 CEST ] [ 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 '' [2026-10-20 19:18:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:18:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-10-20 17:17:02 UTC; omnipath [2026-10-20 19:18:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-10-20 19:18:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.1; ; 2026-10-20 17:17:04 UTC; unix [2026-10-20 19:18:08] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-10-20 19:18:08] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-10-20 19:18:08] [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=2026-10-20; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-10-20 19:18:09] [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] [2026-10-20 19:18:09] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.1(2026-04-03); basilisk 1.23.0(2026-10-20); 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(2026-10-20); 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 4.1.0(2026-10-20); otel 0.2.0(2025-08-29); parallelly 1.48.0(2026-06-29); 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) [2026-10-20 19:18:09] [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 [2026-10-20 19:18:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Contains 1 files. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-10-20 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-10-20 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-10-20 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-10-20 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.24/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-10-20 19:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:09] [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 [2026-10-20 19:18:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-10-20 19:18:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2026-10-20 19:18:30] [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] [2026-10-20 19:18:30] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`. [2026-10-20 19:18:30] [INFO] [OmnipathR] Cache record does not exist: `db://organisms` [2026-10-20 19:18:30] [TRACE] [OmnipathR] Loading database `organisms` from source. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:30] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:30] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-10-20 19:18:30] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-10-20 19:18:30] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-10-20 19:18:30] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-10-20 19:18:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-10-20 19:18:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-10-20 19:18:30] [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] [2026-10-20 19:18:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-10-20 19:18:30] [TRACE] [OmnipathR] Sending HTTP request. [2026-10-20 19:18:30] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-10-20 19:18:30] [TRACE] [OmnipathR] No downlad stats available: no curl handle. [2026-10-20 19:18:30] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 20 Oct 2026 17:18:30 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, 20 Oct 2026 18:18:30 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-10-20 19:18:31] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-10-20 19:18:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:31] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-10-20 19:18:31] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-10-20 19:18:31] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-10-20 19:18:31] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:18:31] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-10-20 19:18:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:31] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-10-20 19:18:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-10-20 19:18:31] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:18:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-10-20 19:18:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-10-20 19:18:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-10-20 19:18:31] [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] [2026-10-20 19:18:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-10-20 19:18:32] [TRACE] [OmnipathR] Downloaded 34.1 Kb in 0.400231s from omabrowser.org (85.2 Kb/s); Redirect: 0.133972s, DNS look up: 0.015324s, Connection: 0.03413s, Pretransfer: 0.130261s, First byte at: 0.397562s [2026-10-20 19:18:32] [TRACE] [OmnipathR] HTTP headers: HTTP/2 302 ; date: Tue, 20 Oct 2026 17:18:31 GMT; content-type: text/html; charset=utf-8; location: https://zenodo.org/records/20922901/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; vary: Cookie; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=4f5ee92cb3367ff8; expires=Thu, 19-Oct-2028 17:18:31 UTC; Path=/; 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=IGbuCt1%2BJz3o5Ja06DjIKj3ndoNjycygru7wQI5sbiI9bRXV%2Fz7rLs3NbjzHrLyjJdqK8LElbdzRxiKaEzpFnyPw6JHtRtoNRwPZhhUBGO2nBoWv6IXyxdTegi3eYioR"}]}; cf-ray: a4d9aea90d04254d-FRA; HTTP/1.1 200 OK; server: nginx; date: Tue, 20 Oct 2026 17:18:32 GMT; content-type: text/plain; charset=utf-8; transfer-encoding: chunked; vary: Accept-Encoding; content-disposition: attachment; filename=oma-species.txt; set-cookie: session=746f2a1395941919_6ad7a268.p1eI0BpQ8FYCxWGwMj9lnZVP-a0; Expires=Sun, 25 Oct 2026 17:18:32 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: 1792516773; retry-after: 60; strict-transport-security: max-age=31556926; includeSubDomains; referrer-policy: strict-origin-when-cross-origin; x-source: files-primary; content-encoding: gzip [2026-10-20 19:18:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-10-20 19:18:32] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-10-20 19:18:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-10-20 19:18:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-10-20 19:18:32] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. Quitting from liana_custom_op.Rmd:115-142 [curation_effort] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map()`: ℹ In index: 1. Caused by error in `map()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─... %>% mutate(curated_flag = 1) 2. ├─dplyr::mutate(., curated_flag = 1) 3. ├─dplyr::distinct(.) 4. ├─dplyr::select(., source_genesymbol, target_genesymbol) 5. ├─liana:::decomplexify(.) 6. │ └─columns %>% ... 7. ├─purrr::map(...) 8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─liana (local) .f(.x[[i]], ...) 13. │ └─... %>% ... 14. ├─dplyr::mutate(...) 15. ├─dplyr::distinct(.) 16. ├─tidyr::drop_na(., all_of(col)) 17. ├─tidyr::pivot_longer(...) 18. ├─tidyr::separate(...) 19. ├─dplyr::mutate(...) 20. ├─OmnipathR::curated_ligand_receptor_interactions(...) 21. │ └─... %>% distinct(across(everything())) 22. ├─dplyr::distinct(., across(everything())) 23. ├─... %>% with_references(resources = curated_resources) 24. ├─OmnipathR::with_references(., resources = curated_resources) 25. │ └─... %>% distinct(across(everything())) 26. ├─dplyr::distinct(., across(everything())) 27. ├─dplyr::bind_rows(.) 28. │ └─rlang::list2(...) 29. ├─purrr::map(., .with_references, data = data) 30. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 31. │ ├─purrr:::with_indexed_errors(...) 32. │ │ └─base::withCallingHandlers(...) 33. │ ├─purrr:::call_with_cleanup(...) 34. │ └─OmnipathR (local) .f(.x[[i]], ...) 35. │ └─data %>% filter(predicate(references)) 36. ├─dplyr::filter(., predicate(references)) 37. ├─OmnipathR::import_post_translational_interactions(...) 38. │ └─OmnipathR::post_translational(...) 39. │ ├─rlang::exec(omnipath_query, !!!args) 40. │ └─OmnipathR (local) ``(resources = ``, query_type = "interactions", datasets = ``) 41. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 42. ├─OmnipathR:::omnipath_check_param(.) 43. │ └─param$organisms %<>% map_int(ncbi_taxid) 44. ├─purrr::map_int(., ncbi_taxid) 45. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 46. │ ├─purrr:::with_indexed_errors(...) 47. │ │ └─base::withCallingHandlers(...) 48. │ ├─purrr:::call_with_cleanup(...) 49. │ └─OmnipathR (local) .f(.x[[i]], ...) 50. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 51. ├─purrr::map_int(., taxon_name, "ncbi") 52. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 53. │ ├─purrr:::with_indexed_errors(...) 54. │ │ └─base::withCallingHandlers(...) 55. │ ├─purrr:::call_with_cleanup(...) 56. │ └─OmnipathR (local) .f(.x[[i]], ...) 57. │ ├─... %>% if_null_len0(NA) 58. │ └─OmnipathR::get_db("organisms") 59. │ └─OmnipathR::load_db(key, param = param, reload = reload) 60. │ ├─rlang::exec(loader, !!!param) 61. │ └─OmnipathR (local) ``() 62. │ └─... %>% ... 63. ├─OmnipathR:::if_null_len0(., NA) 64. │ └─value1 %>% is_empty_2 %>% if (value2) value1 65. ├─OmnipathR:::is_empty_2(.) 66. │ └─value %>% ... 67. ├─dplyr::pull(., name_type) 68. ├─dplyr::filter(...) 69. ├─dplyr::mutate(...) 70. ├─dplyr::full_join(...) 71. ├─dplyr::full_join(...) 72. ├─dplyr:::full_join.data.frame(...) 73. │ └─dplyr:::join_mutate(...) 74. │ └─dplyr:::join_cols(...) 75. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 76. │ └─rlang::abort(bullets, call = error_call) 77. │ └─rlang:::signal_abort(cnd, .file) 78. │ └─base::signalCondition(cnd) 79. ├─purrr (local) ``(``) 80. │ └─cli::cli_abort(...) 81. │ └─rlang::abort(...) 82. │ └─rlang:::signal_abort(cnd, .file) 83. │ └─base::signalCondition(cnd) 84. ├─purrr (local) ``(``) 85. │ └─cli::cli_abort(...) 86. │ └─rlang::abort(...) 87. │ └─rlang:::signal_abort(cnd, .file) 88. │ └─base::signalCondition(cnd) 89. └─purrr (local) ``(``) 90. └─cli::cli_abort(...) --- Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─... %>% mutate(curated_flag = 1) 2. ├─dplyr::mutate(., curated_flag = 1) 3. ├─dplyr::distinct(.) 4. ├─dplyr::select(., source_genesymbol, target_genesymbol) 5. ├─liana:::decomplexify(.) 6. │ └─columns %>% ... 7. ├─purrr::map(...) 8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─liana (local) .f(.x[[i]], ...) 13. │ └─... %>% ... 14. ├─dplyr::mutate(...) 15. ├─dplyr::distinct(.) 16. ├─tidyr::drop_na(., all_of(col)) 17. ├─tidyr::pivot_longer(...) 18. ├─tidyr::separate(...) 19. ├─dplyr::mutate(...) 20. ├─OmnipathR::curated_ligand_receptor_interactions(...) 21. │ └─... %>% distinct(across(everything())) 22. ├─dplyr::distinct(., across(everything())) 23. ├─... %>% with_references(resources = curated_resources) 24. ├─OmnipathR::with_references(., resources = curated_resources) 25. │ └─... %>% distinct(across(everything())) 26. ├─dplyr::distinct(., across(everything())) 27. ├─dplyr::bind_rows(.) 28. │ └─rlang::list2(...) 29. ├─purrr::map(., .with_references, data = data) 30. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 31. │ ├─purrr:::with_indexed_errors(...) 32. │ │ └─base::withCallingHandlers(...) 33. │ ├─purrr:::call_with_cleanup(...) 34. │ └─OmnipathR (local) .f(.x[[i]], ...) 35. │ └─data %>% filter(predicate(references)) 36. ├─dplyr::filter(., predicate(references)) 37. ├─OmnipathR::import_post_translational_interactions(...) 38. │ └─OmnipathR::post_translational(...) 39. │ ├─rlang::exec(omnipath_query, !!!args) 40. │ └─OmnipathR (local) ``(resources = ``, query_type = "interactions", datasets = ``) 41. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 42. ├─OmnipathR:::omnipath_check_param(.) 43. │ └─param$organisms %<>% map_int(ncbi_taxid) 44. ├─purrr::map_int(., ncbi_taxid) 45. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 46. │ ├─purrr:::with_indexed_errors(...) 47. │ │ └─base::withCallingHandlers(...) 48. │ ├─purrr:::call_with_cleanup(...) 49. │ └─OmnipathR (local) .f(.x[[i]], ...) 50. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 51. ├─purrr::map_int(., taxon_name, "ncbi") 52. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 53. │ ├─purrr:::with_indexed_errors(...) 54. │ │ └─base::withCallingHandlers(...) 55. │ ├─purrr:::call_with_cleanup(...) 56. │ └─OmnipathR (local) .f(.x[[i]], ...) 57. │ ├─... %>% if_null_len0(NA) 58. │ └─OmnipathR::get_db("organisms") 59. │ └─OmnipathR::load_db(key, param = param, reload = reload) 60. │ ├─rlang::exec(loader, !!!param) 61. │ └─OmnipathR (local) ``() 62. │ └─... %>% ... 63. ├─OmnipathR:::if_null_len0(., NA) 64. │ └─value1 %>% is_empty_2 %>% if (value2) value1 65. ├─OmnipathR:::is_empty_2(.) 66. │ └─value %>% ... 67. ├─dplyr::pull(., name_type) 68. ├─dplyr::filter(...) 69. ├─dplyr::mutate(...) 70. ├─dplyr::full_join(...) 71. ├─dplyr::full_join(...) 72. ├─dplyr:::full_join.data.frame(...) 73. │ └─dplyr:::join_mutate(...) 74. │ └─dplyr:::join_cols(...) 75. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 76. │ └─rlang::abort(bullets, call = error_call) 77. │ └─rlang:::signal_abort(cnd, .file) 78. │ └─base::signalCondition(cnd) 79. └─purrr (local) ``(``) 80. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─... %>% mutate(curated_flag = 1) 2. ├─dplyr::mutate(., curated_flag = 1) 3. ├─dplyr::distinct(.) 4. ├─dplyr::select(., source_genesymbol, target_genesymbol) 5. ├─liana:::decomplexify(.) 6. │ └─columns %>% ... 7. ├─purrr::map(...) 8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─liana (local) .f(.x[[i]], ...) 13. │ └─... %>% ... 14. ├─dplyr::mutate(...) 15. ├─dplyr::distinct(.) 16. ├─tidyr::drop_na(., all_of(col)) 17. ├─tidyr::pivot_longer(...) 18. ├─tidyr::separate(...) 19. ├─dplyr::mutate(...) 20. ├─OmnipathR::curated_ligand_receptor_interactions(...) 21. │ └─... %>% distinct(across(everything())) 22. ├─dplyr::distinct(., across(everything())) 23. ├─... %>% with_references(resources = curated_resources) 24. ├─OmnipathR::with_references(., resources = curated_resources) 25. │ └─... %>% distinct(across(everything())) 26. ├─dplyr::distinct(., across(everything())) 27. ├─dplyr::bind_rows(.) 28. │ └─rlang::list2(...) 29. ├─purrr::map(., .with_references, data = data) 30. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 31. │ ├─purrr:::with_indexed_errors(...) 32. │ │ └─base::withCallingHandlers(...) 33. │ ├─purrr:::call_with_cleanup(...) 34. │ └─OmnipathR (local) .f(.x[[i]], ...) 35. │ └─data %>% filter(predicate(references)) 36. ├─dplyr::filter(., predicate(references)) 37. ├─OmnipathR::import_post_translational_interactions(...) 38. │ └─OmnipathR::post_translational(...) 39. │ ├─rlang::exec(omnipath_query, !!!args) 40. │ └─OmnipathR (local) ``(resources = ``, query_type = "interactions", datasets = ``) 41. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 42. ├─OmnipathR:::omnipath_check_param(.) 43. │ └─param$organisms %<>% map_int(ncbi_taxid) 44. ├─purrr::map_int(., ncbi_taxid) 45. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 46. │ ├─purrr:::with_indexed_errors(...) 47. │ │ └─base::withCallingHandlers(...) 48. │ ├─purrr:::call_with_cleanup(...) 49. │ └─OmnipathR (local) .f(.x[[i]], ...) 50. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 51. ├─purrr::map_int(., taxon_name, "ncbi") 52. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 53. │ ├─purrr:::with_indexed_errors(...) 54. │ │ └─base::withCallingHandlers(...) 55. │ ├─purrr:::call_with_cleanup(...) 56. │ └─OmnipathR (local) .f(.x[[i]], ...) 57. │ ├─... %>% if_null_len0(NA) 58. │ └─OmnipathR::get_db("organisms") 59. │ └─OmnipathR::load_db(key, param = param, reload = reload) 60. │ ├─rlang::exec(loader, !!!param) 61. │ └─OmnipathR (local) ``() 62. │ └─... %>% ... 63. ├─OmnipathR:::if_null_len0(., NA) 64. │ └─value1 %>% is_empty_2 %>% if (value2) value1 65. ├─OmnipathR:::is_empty_2(.) 66. │ └─value %>% ... 67. ├─dplyr::pull(., name_type) 68. ├─dplyr::filter(...) 69. ├─dplyr::mutate(...) 70. ├─dplyr::full_join(...) 71. ├─dplyr::full_join(...) 72. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_custom_op.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- 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 [2026-10-20 19:21:58] [TRACE] [OmnipathR] Bypassing call: `homologene_raw()`. [2026-10-20 19:21:58] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. 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: 2026-10-20 19:21:59 CEST ]