[ Started: 2025-03-03 00:14:17 CET ] [ decoupleR v2.9.7 for BioC-3.21 from https://github.com/saezlab/decoupleR@devel (930b765 2025-02-15 00:00:59) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown Warning in png(..., res = dpi, units = "in") : unable to open connection to X11 display '' Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2025-03-03 00:14:34] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:14:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:25:41 UTC; omnipath [2025-03-03 00:14:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:14:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:25:42 UTC; unix [2025-03-03 00:14:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:14:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:14:34] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:14:34] [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] [2025-03-03 00:14:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.25(2024-08-28); BiocParallel 1.41.2(2025-02-19); BiocStyle 2.35.0(2024-10-29); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); 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); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-03-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.33.2(2024-12-19); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); ggplot2 3.5.1(2024-04-23); ggrepel 0.9.6(2024-09-07); 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 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.5(2024-09-20); magrittr 2.0.3(2022-03-30); Matrix 1.7-2(2025-01-23); memoise 2.0.1(2021-11-26); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-01); parallelly 1.42.0(2025-01-30); pheatmap 1.0.12(2019-01-04); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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 1.4.4(2025-02-27); RefManageR 1.4.0(2022-09-30); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tinytex 0.56(2025-02-26); tzdb 0.4.0(2023-05-12); utf8 1.2.4(2023-10-22); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-03 00:14:34] [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 [2025-03-03 00:14:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Contains 1 files. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [TRACE] [OmnipathR] Cache locked: FALSE [2025-03-03 00:14:34] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-03-03 00:14:34] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways. [2025-03-03 00:14:34] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:34] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-03-03 00:14:34] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:14:34] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-03-03 00:14:34] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-03-03 00:14:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-03 00:14:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:14:34] [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] [2025-03-03 00:14:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-03 00:14:34] [TRACE] [OmnipathR] Sending HTTP request. [2025-03-03 00:14:35] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-03-03 00:14:35] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 0.45474s from www.ensembl.org (68 Kb/s); Redirect: 0s, DNS look up: 0.0117s, Connection: 0.030264s, Pretransfer: 0.087281s, First byte at: 0.437059s [2025-03-03 00:14:35] [TRACE] [OmnipathR] Response headers: [Date=Sun, 02 Mar 2025 23:14:34 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31650,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=Mon, 03 Mar 2025 23:14:34 GMT,Set-cookie=ENSEMBL_HINX_SESSION=a4315c4dc2db2399099938da6814005a01e0862a29d9ff3bd765022e; 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=Mon, 03 Mar 2025 23:14:34 GMT,Set-cookie=ENSEMBL_HINX_SESSION=a4315c4dc2db2399099938da6814005a01e0862a29d9ff3bd765022e; 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-p1m2-34.ebi.ac.uk] [2025-03-03 00:14:35] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-03-03 00:14:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:35] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:14:35] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:14:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:14:35] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:14:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-03-03 00:14:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:14:35] [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] [2025-03-03 00:14:35] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.105199s from omabrowser.org (1 Mb/s); Redirect: 0s, DNS look up: 0.001116s, Connection: 0.011768s, Pretransfer: 0.044548s, First byte at: 0.057803s [2025-03-03 00:14:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-03 00:14:35] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-03-03 00:14:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-03-03 00:14:35] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-03 00:14:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-03-03 00:14:35] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:14:35] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:14:35] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-03-03 00:14:35] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2025-03-03 00:14:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:35] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:35] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:35] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:37] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-03-03 00:14:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:37] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2025-03-03 00:14:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-03-03 00:14:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-03-03 00:14:39] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2025-03-03 00:14:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:39] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2025-03-03 00:14:39] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Quitting from lines 186-199 [barplot] (pw_bk.Rmd) Error: processing vignette 'pw_bk.Rmd' failed with diagnostics: R: geometry does not contain image `/tmp/RtmpwHcmSv/Rbuild29a8237e090a1e/decoupleR/vignettes/pw_bk_files/figure-html/barplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534 --- failed re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Quitting from lines 67-68 [umap] (pw_sc.Rmd) Error: processing vignette 'pw_sc.Rmd' failed with diagnostics: R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274 --- failed re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2025-03-03 00:14:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-03 00:14:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-03-03 00:14:46] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:14:46] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:14:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:14:46] [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] [2025-03-03 00:14:46] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 1/3); error: cannot open the connection [2025-03-03 00:14:51] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:14:51] [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] [2025-03-03 00:14:51] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 2/3); error: cannot open the connection [2025-03-03 00:14:56] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-03 00:14:56] [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] [2025-03-03 00:14:56] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` (attempt 3/3); error: cannot open the connection [2025-03-03 00:14:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:25:41 UTC; omnipath [2025-03-03 00:14:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:14:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:25:42 UTC; unix [2025-03-03 00:14:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:14:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:14:56] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:14:56] [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] [2025-03-03 00:14:57] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.25(2024-08-28); BiocParallel 1.41.2(2025-02-19); BiocStyle 2.35.0(2024-10-29); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); 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); cli 3.6.4(2025-02-13); cluster 2.1.8(2024-12-11); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-03-02); deldir 2.0-4(2024-02-28); digest 0.6.37(2024-08-19); 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); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.33.2(2024-12-19); fitdistrplus 1.2-2(2025-01-07); fs 1.6.5(2024-10-30); future 1.34.0(2024-07-29); future.apply 1.11.3(2024-10-27); generics 0.1.3(2022-07-05); ggplot2 3.5.1(2024-04-23); ggrepel 0.9.6(2024-09-07); ggridges 0.5.6(2024-01-23); globals 0.16.3(2024-03-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); KernSmooth 2.23-26(2025-01-01); knitr 1.49(2024-11-08); labeling 0.4.3(2023-08-29); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.5(2024-09-20); magrittr 2.0.3(2022-03-30); MASS 7.3-64(2025-01-04); Matrix 1.7-2(2025-01-23); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); miniUI 0.1.1.1(2018-05-18); munsell 0.5.1(2024-04-01); nlme 3.1-167(2025-01-27); OmnipathR 3.15.11(2025-03-01); parallelly 1.42.0(2025-01-30); patchwork 1.3.0(2024-09-16); pbapply 1.7-2(2023-06-27); pheatmap 1.0.12(2019-01-04); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); plotly 4.10.4(2024-01-13); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 0.15.1(2024-11-22); promises 1.3.2(2024-11-28); 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); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.41.0(2025-02-24); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.3.9(2024-12-03); Rtsne 0.17(2023-12-07); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); scales 1.3.0(2023-11-28); scattermore 1.2(2023-06-12); sctransform 0.4.1(2023-10-19); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); Seurat 5.2.1(2025-01-24); SeuratObject 5.0.2(2024-05-08); shiny 1.10.0(2024-12-14); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-4(2024-11-15); spatstat.explore 3.3-4(2025-01-08); spatstat.geom 3.3-5(2025-01-18); spatstat.random 3.3-2(2024-09-18); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-1(2024-11-05); spatstat.utils 3.1-2(2025-01-08); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); survival 3.8-3(2024-12-17); tensor 1.5(2012-05-05); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tinytex 0.56(2025-02-26); tzdb 0.4.0(2023-05-12); utf8 1.2.4(2023-10-22); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01); zoo 1.8-13(2025-02-22) [2025-03-03 00:14:57] [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 [2025-03-03 00:14:57] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`; error: cannot open the connection [2025-03-03 00:14:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-01 23:25:41 UTC; omnipath [2025-03-03 00:14:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-03 00:14:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-01 23:25:42 UTC; unix [2025-03-03 00:14:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-03 00:14:57] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-03 00:14:57] [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=2025-03-03; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-03 00:14:57] [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] [2025-03-03 00:14:57] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.25(2024-08-28); BiocParallel 1.41.2(2025-02-19); BiocStyle 2.35.0(2024-10-29); bit 4.5.0.1(2024-12-03); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.42(2025-01-07); 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); cli 3.6.4(2025-02-13); cluster 2.1.8(2024-12-11); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-03-02); deldir 2.0-4(2024-02-28); digest 0.6.37(2024-08-19); 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); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.33.2(2024-12-19); fitdistrplus 1.2-2(2025-01-07); fs 1.6.5(2024-10-30); future 1.34.0(2024-07-29); future.apply 1.11.3(2024-10-27); generics 0.1.3(2022-07-05); ggplot2 3.5.1(2024-04-23); ggrepel 0.9.6(2024-09-07); ggridges 0.5.6(2024-01-23); globals 0.16.3(2024-03-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.0(2025-01-18); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 1.9.0(2025-02-19); KernSmooth 2.23-26(2025-01-01); knitr 1.49(2024-11-08); labeling 0.4.3(2023-08-29); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.5(2024-09-20); magrittr 2.0.3(2022-03-30); MASS 7.3-64(2025-01-04); Matrix 1.7-2(2025-01-23); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); miniUI 0.1.1.1(2018-05-18); munsell 0.5.1(2024-04-01); nlme 3.1-167(2025-01-27); OmnipathR 3.15.11(2025-03-01); parallelly 1.42.0(2025-01-30); patchwork 1.3.0(2024-09-16); pbapply 1.7-2(2023-06-27); pheatmap 1.0.12(2019-01-04); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); plotly 4.10.4(2024-01-13); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 0.15.1(2024-11-22); promises 1.3.2(2024-11-28); 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); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.4(2025-02-27); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.41.0(2025-02-24); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.3.9(2024-12-03); Rtsne 0.17(2023-12-07); rvest 1.0.4(2024-02-12); sass 0.4.9(2024-03-15); scales 1.3.0(2023-11-28); scattermore 1.2(2023-06-12); sctransform 0.4.1(2023-10-19); selectr 0.4-2(2019-11-20); sessioninfo 1.2.3(2025-02-05); Seurat 5.2.1(2025-01-24); SeuratObject 5.0.2(2024-05-08); shiny 1.10.0(2024-12-14); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-4(2024-11-15); spatstat.explore 3.3-4(2025-01-08); spatstat.geom 3.3-5(2025-01-18); spatstat.random 3.3-2(2024-09-18); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-1(2024-11-05); spatstat.utils 3.1-2(2025-01-08); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); survival 3.8-3(2024-12-17); tensor 1.5(2012-05-05); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tinytex 0.56(2025-02-26); tzdb 0.4.0(2023-05-12); utf8 1.2.4(2023-10-22); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.5(2023-12-05); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01); zoo 1.8-13(2025-02-22) [2025-03-03 00:14:57] [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 [2025-03-03 00:14:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-03 00:14:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:57] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`. [2025-03-03 00:14:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-03-03 00:14:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-03-03 00:14:57] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1] [2025-03-03 00:14:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-03 00:14:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-03 00:14:57] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`. [2025-03-03 00:14:57] [SUCCESS] [OmnipathR] Downloaded 2 interactions. [2025-03-03 00:14:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-03 00:14:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-03-03 00:14:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-03 00:14:57] [TRACE] [OmnipathR] Orthology targets: [2025-03-03 00:14:57] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-03-03 00:14:58] [ERROR] [OmnipathR] [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. Quitting from lines 118-120 [collectri] (tf_bk.Rmd) Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. --- failed re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown Warning: ImageMagick was built without librsvg which causes poor qualty of SVG rendering. For better results use image_read_svg() which uses the rsvg package. Quitting from lines 67-68 [umap] (tf_sc.Rmd) Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274 --- failed re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-03-03 00:14:58 CET ]