[ Started: 2025-04-04 00:56:57 CEST ]
[ 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
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-04-03 22:17:01 UTC; omnipath
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-03 22:17:02 UTC; unix
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.12
[2025-04-04 00:57:13] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-04-04 00:57:13] [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=2025-04-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-04-04 00:57:13] [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]
[2025-04-04 00:57:13] [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 1.41.5(2025-04-01); BiocStyle 2.35.0(2024-10-29); bit 4.6.0(2025-03-06); 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 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-04-03); 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 1.33.4(2025-03-20); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); 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 2.8.6(2025-03-23); 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 3.15.12(2025-04-03); parallelly 1.43.0(2025-03-24); 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 1.4.5(2025-03-07); 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 1.8.7(2025-03-27); 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 0.5.0(2025-03-15); utf8 1.2.4(2023-10-22); 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); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-04 00:57:13] [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
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.21/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:13] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-04 00:57:14] [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]
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Downloaded 30.9 Kb in 0.217884s from www.ensembl.org (141.9 Kb/s); Redirect: 0s, DNS look up: 0.018755s, Connection: 0.037269s, Pretransfer: 0.100641s, First byte at: 0.200365s
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Thu, 03 Apr 2025 22:57:14 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31669; 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=Fri, 04 Apr 2025 22:57:14 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c83e9edb03f970910e5e89cd683e2c4a006faf9d4e5c657bacaff83a; 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=Fri, 04 Apr 2025 22:57:14 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c83e9edb03f970910e5e89cd683e2c4a006faf9d4e5c657bacaff83a; 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-p1m2-33.ebi.ac.uk
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Response headers: [Date=Thu, 03 Apr 2025 22:57:14 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31669,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=Fri, 04 Apr 2025 22:57:14 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c83e9edb03f970910e5e89cd683e2c4a006faf9d4e5c657bacaff83a; 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=Fri, 04 Apr 2025 22:57:14 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c83e9edb03f970910e5e89cd683e2c4a006faf9d4e5c657bacaff83a; 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-p1m2-33.ebi.ac.uk]
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-04 00:57:14] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-04 00:57:14] [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]
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.061714s from omabrowser.org (140.8 Kb/s); Redirect: 0s, DNS look up: 0.001012s, Connection: 0.010699s, Pretransfer: 0.048784s, First byte at: 0.06157s
[2025-04-04 00:57:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 03 Apr 2025 22:57:14 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
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Orthology targets: 
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-04 00:57:15] [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]
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099505s from omnipathdb.org (157.4 Kb/s); Redirect: 0s, DNS look up: 0.000909s, Connection: 0.022326s, Pretransfer: 0.055637s, First byte at: 0.099198s
[2025-04-04 00:57:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 03 Apr 2025 22:57:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 03 Apr 2025 23:57:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-04 00:57:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-04 00:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:17] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-04-04 00:57:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-04-04 00:57:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-04-04 00:57:19] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-04-04 00:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:19] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-04-04 00:57:19] [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 pw_bk.Rmd:185-199 [barplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: geometry does not contain image `/tmp/RtmpW0woJ4/Rbuild33b9582ae40c55/decoupleR/vignettes/pw_bk_files/figure-html/barplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   └─knitr:::run_hooks(before = FALSE, options, env)
 18. │                     └─base::do.call(hook, args, envir = envir)
 19. └─knitr (local) `<fn>`(...)
 20.   ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
 21.   │ └─knitr:::in_dir(d, expr)
 22.   └─knitr::plot_crop(f)
 23.     ├─magick::image_write(magick::image_trim(img), x)
 24.     │ └─magick:::assert_image(image)
 25.     └─magick::image_trim(img)
 26.       └─magick:::magick_image_trim(image, fuzz)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
R: geometry does not contain image `/tmp/RtmpW0woJ4/Rbuild33b9582ae40c55/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 pw_sc.Rmd:66-68 [umap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   └─knitr:::run_hooks(before = FALSE, options, env)
 18. │                     └─base::do.call(hook, args, envir = envir)
 19. └─knitr (local) `<fn>`(...)
 20.   ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
 21.   │ └─knitr:::in_dir(d, expr)
 22.   └─knitr::plot_crop(f)
 23.     └─magick::image_write(magick::image_trim(img), x)
 24.       └─magick:::magick_image_write(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Orthology targets: 
[2025-04-04 00:57:26] [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`
[2025-04-04 00:57:26] [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`
[2025-04-04 00:57:26] [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`
[2025-04-04 00:57:26] [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`
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-04 00:57:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-04 00:57:26] [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]
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094985s from omnipathdb.org (164.9 Kb/s); Redirect: 0s, DNS look up: 0.001083s, Connection: 0.021068s, Pretransfer: 0.054509s, First byte at: 0.09458s
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 03 Apr 2025 22:57:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 03 Apr 2025 23:57:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-04 00:57:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:26] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-04-04 00:57:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-04-04 00:57:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-04-04 00:57:27] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-04-04 00:57:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:27] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-04-04 00:57:29] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Orthology targets: 
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-04-04 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]
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Downloaded 9.5 Kb in 0.080267s from omnipathdb.org (118.3 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.020849s, Pretransfer: 0.054216s, First byte at: 0.079985s
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 03 Apr 2025 22:57:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 03 Apr 2025 23:57:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-04 00:57:29] [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`
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:29] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-04-04 00:57:29] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-04 00:57:29] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-04-04 00:57:29] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-04-04 00:57:30] [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 tf_bk.Rmd:189-217 [barplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: geometry does not contain image `/tmp/RtmpW0woJ4/Rbuild33b9582ae40c55/decoupleR/vignettes/tf_bk_files/figure-html/barplot-1.svg' @ warning/attribute.c/GetImageBoundingBox/534
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   └─knitr:::run_hooks(before = FALSE, options, env)
 18. │                     └─base::do.call(hook, args, envir = envir)
 19. └─knitr (local) `<fn>`(...)
 20.   ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
 21.   │ └─knitr:::in_dir(d, expr)
 22.   └─knitr::plot_crop(f)
 23.     ├─magick::image_write(magick::image_trim(img), x)
 24.     │ └─magick:::assert_image(image)
 25.     └─magick::image_trim(img)
 26.       └─magick:::magick_image_trim(image, fuzz)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
R: geometry does not contain image `/tmp/RtmpW0woJ4/Rbuild33b9582ae40c55/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 tf_sc.Rmd:66-68 [umap]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
---
Backtrace:
     ▆
  1. ├─tools::buildVignettes(dir = ".", tangle = TRUE)
  2. │ ├─base::tryCatch(...)
  3. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  6. │ └─engine$weave(file, quiet = quiet, encoding = enc)
  7. │   └─knitr:::vweave_rmarkdown(...)
  8. │     └─rmarkdown::render(...)
  9. │       └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10. │         └─knitr:::process_file(text, output)
 11. │           ├─xfun:::handle_error(...)
 12. │           ├─base::withCallingHandlers(...)
 13. │           └─knitr:::process_group(group)
 14. │             └─knitr:::call_block(x)
 15. │               └─knitr:::block_exec(params)
 16. │                 └─knitr:::eng_r(options)
 17. │                   └─knitr:::run_hooks(before = FALSE, options, env)
 18. │                     └─base::do.call(hook, args, envir = envir)
 19. └─knitr (local) `<fn>`(...)
 20.   ├─knitr:::in_base_dir(for (f in get_plot_files()) plot_crop(f))
 21.   │ └─knitr:::in_dir(d, expr)
 22.   └─knitr::plot_crop(f)
 23.     └─magick::image_write(magick::image_trim(img), x)
 24.       └─magick:::magick_image_write(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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: 2025-04-04 00:57:41 CEST ]