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###
### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
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* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-03
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-03 20:09:31 UTC; unix
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-03; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-03 17:14:48] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-03 17:14:48] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.2(2026-02-03); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2026-03-03); BiocStyle 2.39.0(2026-03-03); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.17.0(2026-03-03); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.37.4(2026-03-03); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.7(2026-02-25); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-03-03); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tinytex 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-03 17:14:48] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-03 17:14:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-03 17:14:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-03 17:14:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:50] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-03 17:14:50] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:50] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:50] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-03 17:14:50] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-03 17:14:50] [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]
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.609533s from rescued.omnipathdb.org (65.4 Kb/s); Redirect: 0s, DNS look up: 0.023269s, Connection: 0.024194s, Pretransfer: 0.326963s, First byte at: 0.470451s
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 03 Mar 2026 22:14:50 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Tue, 03 Mar 2026 23:14:50 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-03 17:14:50] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Tue, 03 Mar 2026 22:14:50 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 03 Mar 2026 23:14:50 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-03 17:14:51] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:51] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-03 17:14:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-03 17:14:51] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-03 17:14:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-03 17:14:51] [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]
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.44225s from omabrowser.org (17.1 Kb/s); Redirect: 0s, DNS look up: 0.051922s, Connection: 0.06471s, Pretransfer: 0.104118s, First byte at: 0.442015s
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 03 Mar 2026 22:14:52 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=bs3TW7D7nUpBiCLaUWz4DTasrQVh2QVLzJ2h9d7OOmPoCLbFB4nC62%2BapB%2BrX5JGZdzMqoCF9HW2SovyB2qOuIkDjj1rktm%2BeafOMM3Z"}]}; cf-ray: 9d6bff1d1b90c98c-IAD; alt-svc: h3=":443"; ma=86400
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-03 17:14:52] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-03 17:14:52] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:14:52] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-03 17:14:52] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-03 17:14:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-03 17:15:24] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:15:24] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:15:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:15:24] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-03 17:15:25] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:15:25] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-03 17:15:25] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:15:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-03 17:15:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-03 17:15:26] [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]
[2026-03-03 17:15:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-03 17:15:45] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 18.228518s from omnipathdb.org (878 bytes/s); Redirect: 0s, DNS look up: 0.001442s, Connection: 0.002198s, Pretransfer: 0.168875s, First byte at: 18.228097s
[2026-03-03 17:15:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 03 Mar 2026 22:15:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 03 Mar 2026 23:15:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-03 17:16:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:16:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:14] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:16:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-03 17:16:16] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-03 17:16:16] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-03-03 17:16:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:16] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-03-03 17:16:16] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.

Quitting from pw_bk.Rmd:140-145 [sample_mlm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mor_mat[[.target, .source]] <- .weight`:
! [[ ]] subscript out of bounds
---
Backtrace:
    ▆
 1. ├─decoupleR::run_mlm(...)
 2. │ ├─... %>% ungroup()
 3. │ └─decoupleR::.fit_preprocessing(network, mat, center, na.rm, sparse)
 4. └─dplyr::ungroup(.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
[[ ]] subscript out of bounds
--- failed re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2026-03-03 17:16:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:16:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:16:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-03 17:16:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-03 17:16:26] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.

Quitting from pw_sc.Rmd:108-116 [mlm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mor_mat[[.target, .source]] <- .weight`:
! [[ ]] subscript out of bounds
---
Backtrace:
    ▆
 1. ├─decoupleR::run_mlm(...)
 2. │ ├─... %>% ungroup()
 3. │ └─decoupleR::.fit_preprocessing(network, mat, center, na.rm, sparse)
 4. └─dplyr::ungroup(.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'pw_sc.Rmd' failed with diagnostics:
[[ ]] subscript out of bounds
--- failed re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:16:27] [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`
[2026-03-03 17:16:27] [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`
[2026-03-03 17:16:27] [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`
[2026-03-03 17:16:27] [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`
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-03 17:16:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-03 17:16:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-03 17:16:27] [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]
[2026-03-03 17:16:37] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-03 17:16:37] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 9.886501s from omnipathdb.org (1.6 Kb/s); Redirect: 0s, DNS look up: 0.001667s, Connection: 0.01682s, Pretransfer: 0.171844s, First byte at: 9.885179s
[2026-03-03 17:16:37] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 03 Mar 2026 22:16:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 03 Mar 2026 23:16:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-03 17:16:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:40] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-03 17:16:40] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:40] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-03-03 17:16:43] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-03-03 17:16:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:16:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-03-03 17:16:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:16:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:16:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:16:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [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`
[2026-03-03 17:16:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-03 17:16:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-03 17:16:44] [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]
[2026-03-03 17:16:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-03 17:16:45] [TRACE]   [OmnipathR] Downloaded 9.1 Kb in 1.304415s from omnipathdb.org (7 Kb/s); Redirect: 0s, DNS look up: 0.00184s, Connection: 0.002632s, Pretransfer: 0.1568s, First byte at: 1.303505s
[2026-03-03 17:16:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 03 Mar 2026 22:16:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Tue, 03 Mar 2026 23:16:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-03 17:16:46] [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`
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:46] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-03 17:16:46] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:16:46] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-03-03 17:16:46] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-03-03 17:16:47] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
--- finished re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2026-03-03 17:17:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:17:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-03-03 17:17:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:17:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:17:18] [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`
[2026-03-03 17:17:18] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-03 17:17:18] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-03 17:17:22] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-03-03 17:17:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-03 17:17:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-03-03 17:17:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-03 17:17:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-03 17:17:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-03 17:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-03 17:17:23] [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`
[2026-03-03 17:17:23] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-03 17:17:23] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-03-03 17:17:23] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-03-03 17:17:23] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-03-03 17:17:23] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-03-03 17:17:23] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.

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--- finished re-building ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘pw_bk.Rmd’ ‘pw_sc.Rmd’

Error: Vignette re-building failed.
Execution halted