[ Started: 2025-05-02 23:30:39 CEST ] [ liana v0.1.14 for BioC-3.21 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 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 '' [2025-05-02 23:31:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:19] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-05-02 23:31:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-05-02 21:30:19 UTC; omnipath [2025-05-02 23:31:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-05-02 23:31:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-02 21:30:20 UTC; unix [2025-05-02 23:31:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.14 [2025-05-02 23:31:19] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-05-02 23:31:20] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-05-02; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-05-02 23:31:20] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/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] [2025-05-02 23:31:20] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); basilisk 1.21.0(2025-04-25); basilisk.utils 1.21.0(2025-04-16); Biobase 2.68.0(2025-04-15); BiocGenerics 0.54.0(2025-04-15); BiocManager 1.30.25(2024-08-28); BiocStyle 2.36.0(2025-04-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clue 0.3-66(2024-11-13); cluster 2.1.8(2024-12-11); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.24.0(2025-04-15); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); DelayedArray 0.34.1(2025-04-17); digest 0.6.37(2024-08-19); dir.expiry 1.16.0(2025-04-15); doParallel 1.0.17(2022-02-07); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); filelock 1.0.3(2023-12-11); forcats 1.0.0(2023-01-29); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); future 1.40.0(2025-04-10); future.apply 1.11.3(2024-10-27); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-15); GenomeInfoDbData 1.2.14(2025-03-12); GenomicRanges 1.60.0(2025-04-15); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); GlobalOptions 0.1.2(2020-06-10); globals 0.17.0(2025-04-16); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.42.0(2025-04-15); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-6(2024-03-20); liana 0.1.14(2025-05-02); lifecycle 1.0.4(2023-11-07); listenv 0.9.1(2024-01-29); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); MatrixGenerics 1.20.0(2025-04-15); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.15.14(2025-05-02); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 0.15.1(2024-11-22); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reticulate 1.42.0(2025-03-25); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.10(2025-05-02); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-15); S4Vectors 0.46.0(2025-04-15); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); SeuratObject 5.1.0(2025-04-22); shape 1.4.6.1(2024-02-23); SingleCellExperiment 1.30.0(2025-04-15); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); SparseArray 1.8.0(2025-04-15); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-04-30); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); tidyverse 2.0.0(2023-02-22); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.4.0(2025-04-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); XVector 0.48.0(2025-04-15); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-05-02 23:31:20] [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 [2025-05-02 23:31:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Contains 1 files. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-05-02 23:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-05-02 23:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-05-02 23:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-05-02 23:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-05-02 23:31:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:20] [TRACE] [OmnipathR] Cache locked: FALSE Quitting from liana_cc2tensor.Rmd:84-88 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! failed to load resource name: EH2259 title: Kang18_8vs8 reason: invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- Backtrace: ▆ 1. ├─eh[["EH2259"]] 2. └─eh[["EH2259"]] 3. └─ExperimentHub (local) .local(x, i, j = j, ...) 4. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose) 5. │ └─base::eval(call, callEnv) 6. │ └─base::eval(call, callEnv) 7. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose) 8. └─AnnotationHub (local) .local(x, i, j = j, ...) 9. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose) 10. └─base::tryCatch(...) 11. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 12. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 13. └─value[[3L]](cond) 14. └─base::tryCatch(...) 15. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 16. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_cc2tensor.Rmd' failed with diagnostics: failed to load resource name: EH2259 title: Kang18_8vs8 reason: invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- failed re-building ‘liana_cc2tensor.Rmd’ --- re-building ‘liana_custom_op.Rmd’ using rmarkdown [2025-05-02 23:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020],query_type=interactions] [2025-05-02 23:31:57] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-05-02 23:31:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:57] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-05-02 23:31:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:57] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-05-02 23:31:57] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-05-02 23:31:57] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-05-02 23:31:57] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-05-02 23:31:57] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-05-02 23:31:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-05-02 23:31:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-02 23:31:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:31:57] [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] [2025-05-02 23:31:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-05-02 23:31:57] [TRACE] [OmnipathR] Sending HTTP request. [2025-05-02 23:31:58] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-05-02 23:31:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:31:58] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 0.248564s from www.ensembl.org (125.1 Kb/s); Redirect: 0s, DNS look up: 0.029761s, Connection: 0.048074s, Pretransfer: 0.128289s, First byte at: 0.225447s [2025-05-02 23:31:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Fri, 02 May 2025 21:31:58 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31837; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Sat, 03 May 2025 21:31:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0872dfd94d651deb08cad60b686453ce0c75762ed60ff13af0a43429; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Sat, 03 May 2025 21:31:57 GMT; Set-cookie: ENSEMBL_HINX_SESSION=0872dfd94d651deb08cad60b686453ce0c75762ed60ff13af0a43429; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk [2025-05-02 23:31:58] [TRACE] [OmnipathR] Response headers: [Date=Fri, 02 May 2025 21:31:58 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31837,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Sat, 03 May 2025 21:31:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0872dfd94d651deb08cad60b686453ce0c75762ed60ff13af0a43429; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Sat, 03 May 2025 21:31:57 GMT,Set-cookie=ENSEMBL_HINX_SESSION=0872dfd94d651deb08cad60b686453ce0c75762ed60ff13af0a43429; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-35.ebi.ac.uk] [2025-05-02 23:31:58] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-05-02 23:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:58] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-05-02 23:31:58] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-05-02 23:31:58] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-05-02 23:31:58] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-05-02 23:31:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-05-02 23:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-05-02 23:31:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-05-02 23:31:58] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-05-02 23:31:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-05-02 23:31:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:31:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:31:58] [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] [2025-05-02 23:31:59] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-05-02 23:31:59] [TRACE] [OmnipathR] Downloaded 5 Kb in 0.078905s from omabrowser.org (63.9 Kb/s); Redirect: 0s, DNS look up: 0.016698s, Connection: 0.027554s, Pretransfer: 0.064882s, First byte at: 0.078812s [2025-05-02 23:31:59] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 02 May 2025 21:31:59 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-05-02 23:31:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-05-02 23:31:59] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-05-02 23:31:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:31:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:31:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-05-02 23:31:59] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-05-02 23:31:59] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:31:59] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:00] [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] [2025-05-02 23:32:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108388s from omnipathdb.org (144.5 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.023662s, Pretransfer: 0.063288s, First byte at: 0.108038s [2025-05-02 23:32:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:00] [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` [2025-05-02 23:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:00] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2025-05-02 23:32:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`. [2025-05-02 23:32:00] [INFO] [OmnipathR] Download ready [key=69503cb1a01671e7c77c0e80e6ca0ce4110a89fe, version=1] [2025-05-02 23:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:00] [INFO] [OmnipathR] Cache item `69503cb1a01671e7c77c0e80e6ca0ce4110a89fe` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:01] [SUCCESS] [OmnipathR] Downloaded 4568 interactions. [2025-05-02 23:32:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellPhoneDB,fields=extra_attrs,query_type=interactions] [2025-05-02 23:32:01] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:01] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [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` [2025-05-02 23:32:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:01] [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] [2025-05-02 23:32:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103163s from omnipathdb.org (151.9 Kb/s); Redirect: 0s, DNS look up: 0.000864s, Connection: 0.022236s, Pretransfer: 0.059813s, First byte at: 0.102756s [2025-05-02 23:32:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:01 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:02] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-05-02 23:32:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`. [2025-05-02 23:32:02] [INFO] [OmnipathR] Download ready [key=ec8c89037e2c920468342c7c2326c74a5474eedc, version=1] [2025-05-02 23:32:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:02] [INFO] [OmnipathR] Cache item `ec8c89037e2c920468342c7c2326c74a5474eedc` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:02] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-05-02 23:32:02] [SUCCESS] [OmnipathR] Downloaded 2879 interactions. [2025-05-02 23:32:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=Cellinker,fields=extra_attrs,query_type=interactions] [2025-05-02 23:32:02] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:02] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [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` [2025-05-02 23:32:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:02] [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] [2025-05-02 23:32:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100002s from omnipathdb.org (156.7 Kb/s); Redirect: 0s, DNS look up: 0.001007s, Connection: 0.019193s, Pretransfer: 0.056676s, First byte at: 0.099639s [2025-05-02 23:32:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:03] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-05-02 23:32:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`. [2025-05-02 23:32:03] [INFO] [OmnipathR] Download ready [key=8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5, version=1] [2025-05-02 23:32:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:03] [INFO] [OmnipathR] Cache item `8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:03] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-05-02 23:32:03] [SUCCESS] [OmnipathR] Downloaded 3765 interactions. [2025-05-02 23:32:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=talklr,fields=extra_attrs,query_type=interactions] [2025-05-02 23:32:03] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:03] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [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` [2025-05-02 23:32:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:03] [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] [2025-05-02 23:32:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105964s from omnipathdb.org (147.9 Kb/s); Redirect: 0s, DNS look up: 0.000749s, Connection: 0.022984s, Pretransfer: 0.06081s, First byte at: 0.1056s [2025-05-02 23:32:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:04] [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` [2025-05-02 23:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:04] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2025-05-02 23:32:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`. [2025-05-02 23:32:04] [INFO] [OmnipathR] Download ready [key=b2de51666493a9c70a7b375972a2557903c14763, version=1] [2025-05-02 23:32:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:04] [INFO] [OmnipathR] Cache item `b2de51666493a9c70a7b375972a2557903c14763` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:04] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-05-02 23:32:04] [SUCCESS] [OmnipathR] Downloaded 2484 interactions. [2025-05-02 23:32:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=CellChatDB,fields=extra_attrs,query_type=interactions] [2025-05-02 23:32:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:05] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [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` [2025-05-02 23:32:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:05] [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] [2025-05-02 23:32:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:05] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100157s from omnipathdb.org (156.4 Kb/s); Redirect: 0s, DNS look up: 0.000907s, Connection: 0.020951s, Pretransfer: 0.058885s, First byte at: 0.099766s [2025-05-02 23:32:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:06] [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` [2025-05-02 23:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:06] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-05-02 23:32:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`. [2025-05-02 23:32:06] [INFO] [OmnipathR] Download ready [key=fedf7fd37a8e863f804aa073f2ae480ff78001e5, version=1] [2025-05-02 23:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:06] [INFO] [OmnipathR] Cache item `fedf7fd37a8e863f804aa073f2ae480ff78001e5` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:06] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-05-02 23:32:06] [SUCCESS] [OmnipathR] Downloaded 1894 interactions. [2025-05-02 23:32:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,query_type=interactions] [2025-05-02 23:32:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:06] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:06] [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` [2025-05-02 23:32:06] [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` [2025-05-02 23:32:06] [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` [2025-05-02 23:32:06] [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` [2025-05-02 23:32:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-05-02 23:32:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-05-02 23:32:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-05-02 23:32:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:06] [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] [2025-05-02 23:32:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09595s from omnipathdb.org (163.3 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.018843s, Pretransfer: 0.059137s, First byte at: 0.095637s [2025-05-02 23:32:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-05-02 23:32:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:07] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-05-02 23:32:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`. [2025-05-02 23:32:07] [INFO] [OmnipathR] Download ready [key=95ee739b50bbfea2c48e5c86a64525084a1dab30, version=1] [2025-05-02 23:32:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:07] [INFO] [OmnipathR] Cache item `95ee739b50bbfea2c48e5c86a64525084a1dab30` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:07] [SUCCESS] [OmnipathR] Downloaded 1796 interactions. [2025-05-02 23:32:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-05-02 23:32:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_function,query_type=annotations] [2025-05-02 23:32:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-05-02 23:32:07] [TRACE] [OmnipathR] Orthology targets: [2025-05-02 23:32:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-05-02 23:32:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-05-02 23:32:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-05-02 23:32:07] [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] [2025-05-02 23:32:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-05-02 23:32:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108314s from omnipathdb.org (144.6 Kb/s); Redirect: 0s, DNS look up: 0.000889s, Connection: 0.020356s, Pretransfer: 0.068423s, First byte at: 0.107975s [2025-05-02 23:32:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 02 May 2025 21:32:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 02 May 2025 22:32:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-05-02 23:32:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&license=academic` [2025-05-02 23:32:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:08] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `unknown` to `started`. [2025-05-02 23:32:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2025-05-02 23:32:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd-1.rds`. [2025-05-02 23:32:08] [INFO] [OmnipathR] Download ready [key=4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd, version=1] [2025-05-02 23:32:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-05-02 23:32:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-05-02 23:32:08] [INFO] [OmnipathR] Cache item `4190db12b9aabca9c0851ec84aa3fbb71b5dfbcd` version 1: status changed from `started` to `ready`. [2025-05-02 23:32:08] [SUCCESS] [OmnipathR] Downloaded 2001 annotation records. [2025-05-02 23:32:08] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::filter_intercell_network(., simplify = FALSE, ...)`. [2025-05-02 23:32:08] [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 in `validObject()`: ! invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- Backtrace: ▆ 1. ├─liana::liana_prep(testdata) 2. └─liana:::liana_prep.Seurat(testdata) 3. └─SingleCellExperiment::SingleCellExperiment(...) 4. └─SingleCellExperiment:::.rse_to_sce(...) 5. └─methods::new(...) 6. ├─methods::initialize(value, ...) 7. └─methods::initialize(value, ...) 8. └─methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_devel.Rmd' failed with diagnostics: invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- failed re-building ‘liana_devel.Rmd’ --- re-building ‘liana_nichenet.Rmd’ using rmarkdown Quitting from liana_nichenet.Rmd:42-50 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `library()`: ! there is no package called 'nichenetr' --- Backtrace: ▆ 1. └─base::library(nichenetr) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_nichenet.Rmd' failed with diagnostics: there is no package called 'nichenetr' --- failed re-building ‘liana_nichenet.Rmd’ --- re-building ‘liana_ortho.Rmd’ using rmarkdown [2025-05-02 23:33:18] [TRACE] [OmnipathR] Bypassing call: `homologene_raw()`. [2025-05-02 23:33:18] [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 in `validObject()`: ! invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- Backtrace: ▆ 1. └─liana::liana_wrap(testdata) 2. ├─liana::liana_prep(...) 3. └─liana:::liana_prep.Seurat(...) 4. └─SingleCellExperiment::SingleCellExperiment(...) 5. └─SingleCellExperiment:::.rse_to_sce(...) 6. └─methods::new(...) 7. ├─methods::initialize(value, ...) 8. └─methods::initialize(value, ...) 9. └─methods::validObject(.Object) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'liana_tutorial.Rmd' failed with diagnostics: invalid class "SingleCellExperiment" object: superclass "ExpData" not defined in the environment of the object's class --- 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: 2025-05-02 23:33:19 CEST ]