[ Started: 2025-03-04 00:57:11 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 [2025-03-04 00:57:27] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-03-04 00:57:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-03-03 23:16:32 UTC; omnipath [2025-03-04 00:57:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-03-04 00:57:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-03 23:16:34 UTC; unix [2025-03-04 00:57:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-04 00:57:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-03-04 00:57:27] [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=2025-03-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-03-04 00:57:27] [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] [2025-03-04 00:57:27] [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(2025-03-03); 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 1.9.1(2025-03-03); 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(2025-03-03); 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) [2025-03-04 00:57:27] [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 [2025-03-04 00:57:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Contains 1 files. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-04 00:57:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:27] [TRACE] [OmnipathR] Cache locked: FALSE [2025-03-04 00:57:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-04 00:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-03-04 00:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-03-04 00:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-03-04 00:57:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-03-04 00:57:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-03-04 00:57:28] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-03-04 00:57:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-03-04 00:57:28] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-03-04 00:57:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-04 00:57:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-04 00:57:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-03-04 00:57:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-03-04 00:57:28] [TRACE] [OmnipathR] Sending HTTP request. [2025-03-04 00:57:28] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-03-04 00:57:28] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.441225s from www.ensembl.org (70.3 Kb/s); Redirect: 0s, DNS look up: 0.086539s, Connection: 0.104969s, Pretransfer: 0.189766s, First byte at: 0.420855s [2025-03-04 00:57:28] [TRACE] [OmnipathR] Response headers: [Date=Mon, 03 Mar 2025 23:57:28 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31757,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=Tue, 04 Mar 2025 23:57:28 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ab131eda6026e21a0b6688e968155be803c67a657780c4e3145ece93; 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=Tue, 04 Mar 2025 23:57:28 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ab131eda6026e21a0b6688e968155be803c67a657780c4e3145ece93; 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] [2025-03-04 00:57:28] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-03-04 00:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:28] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-03-04 00:57:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-03-04 00:57:29] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-03-04 00:57:29] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-03-04 00:57:29] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-03-04 00:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-03-04 00:57:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-04 00:57:29] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-03-04 00:57:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-03-04 00:57:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-04 00:57:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-03-04 00:57:29] [TRACE] [OmnipathR] Downloaded 108 Kb in 0.09883s from omabrowser.org (1.1 Mb/s); Redirect: 0s, DNS look up: 0.000992s, Connection: 0.012413s, Pretransfer: 0.045994s, First byte at: 0.060009s [2025-03-04 00:57:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-03-04 00:57:29] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-03-04 00:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:29] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-03-04 00:57:29] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-03-04 00:57:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-04 00:57:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-03-04 00:57:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-04 00:57:29] [TRACE] [OmnipathR] Orthology targets: [2025-03-04 00:57:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-04 00:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-04 00:57:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-03-04 00:57:31] [TRACE] [OmnipathR] Downloaded 8.9 Mb in 1.022306s from omnipathdb.org (8.7 Mb/s); Redirect: 0s, DNS look up: 0.001034s, Connection: 0.018778s, Pretransfer: 0.067686s, First byte at: 0.103255s [2025-03-04 00:57:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-03-04 00:57:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:31] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2025-03-04 00:57:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-03-04 00:57:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-03-04 00:57:33] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2025-03-04 00:57:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:33] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2025-03-04 00:57:33] [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/RtmpVMb00F/Rbuild2fbe9957928e38/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 [2025-03-04 00:57:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-04 00:57:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-03-04 00:57:41] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-04 00:57:41] [TRACE] [OmnipathR] Orthology targets: [2025-03-04 00:57:41] [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` [2025-03-04 00:57:41] [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` [2025-03-04 00:57:41] [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` [2025-03-04 00:57:41] [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` [2025-03-04 00:57:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-04 00:57:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-04 00:57:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-04 00:57:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-04 00:57:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-03-04 00:57:41] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 0.24708s from omnipathdb.org (5.9 Mb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.021459s, Pretransfer: 0.055615s, First byte at: 0.096759s [2025-03-04 00:57:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-03-04 00:57:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:41] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`. [2025-03-04 00:57:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-03-04 00:57:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-03-04 00:57:42] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1] [2025-03-04 00:57:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:42] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`. [2025-03-04 00:57:43] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2025-03-04 00:57:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-03-04 00:57:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-03-04 00:57:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-03-04 00:57:43] [TRACE] [OmnipathR] Orthology targets: [2025-03-04 00:57:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-03-04 00:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-03-04 00:57:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-03-04 00:57:44] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.075589s from omnipathdb.org (125.6 Kb/s); Redirect: 0s, DNS look up: 0.000906s, Connection: 0.020659s, Pretransfer: 0.054428s, First byte at: 0.075373s [2025-03-04 00:57:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-03-04 00:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:44] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2025-03-04 00:57:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-03-04 00:57:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-03-04 00:57:44] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2025-03-04 00:57:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-04 00:57:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-04 00:57:44] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2025-03-04 00:57:44] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-03-04 00:57:44] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-03-04 00:57:44] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-03-04 00:57:45] [SUCCESS] [OmnipathR] Downloaded 232 interactions. 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 190-217 [barplot] (tf_bk.Rmd) Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: R: geometry does not contain image `/tmp/RtmpVMb00F/Rbuild2fbe9957928e38/decoupleR/vignettes/tf_bk_files/figure-html/barplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534 --- 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: 2025-03-04 00:57:57 CET ]