Multiple platform build/check report for BioC 3.23 - BUILD results for decoupleR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4877
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4570
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BUILD results for decoupleR on kjohnson3

To the developers/maintainers of the decoupleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: decoupleR
Version: 2.17.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
StartedAt: 2026-03-02 16:07:03 -0500 (Mon, 02 Mar 2026)
EndedAt: 2026-03-02 16:08:58 -0500 (Mon, 02 Mar 2026)
EllapsedTime: 115.2 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
###
##############################################################################
##############################################################################


* 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
2026-03-02 16:07:08.160 R[56517:58931603] XType: Using static font registry.
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-02
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-02 20:05:00 UTC; unix
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-02 16:07:15] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-02; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-02 16:07:15] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-02 16:07:15] [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(2026-03-02); BiocStyle 2.39.0(2026-03-02); 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 1.17.8(2025-07-10); DBI 1.3.0(2026-02-25); decoupleR 2.17.0(2026-03-02); 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(2026-03-02); 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 2.9.0(2025-09-08); 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(2026-03-02); 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)
[2026-03-02 16:07:15] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-02 16:07:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:16] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-02 16:07:16] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:16] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:16] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-02 16:07:16] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-02 16:07:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.601453s from rescued.omnipathdb.org (66.3 Kb/s); Redirect: 0s, DNS look up: 0.018448s, Connection: 0.019243s, Pretransfer: 0.317747s, First byte at: 0.462376s
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 21:07:16 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: Mon, 02 Mar 2026 22:07:16 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 02 Mar 2026 21:07:16 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=Mon, 02 Mar 2026 22:07:16 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-02 16:07:17] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:17] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-02 16:07:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:17] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-02 16:07:17] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] Downloaded 4 Kb in 0.413404s from omabrowser.org (9.7 Kb/s); Redirect: 0s, DNS look up: 0.03141s, Connection: 0.044862s, Pretransfer: 0.065589s, First byte at: 0.413265s
[2026-03-02 16:07:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 02 Mar 2026 21:07:17 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=vvee%2BuwFvyuG9relFNt7Z29FA2%2BDDA0Uve4moChp3EnU2Y6%2BKi7ytceSwIPCQnnTC3%2F45hFZv5w38EnJhKXfwi9y%2BbtpvUW2Wkk%2FyaYz"}]}; cf-ray: 9d635ec2a9624406-EWR; alt-svc: h3=":443"; ma=86400
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-02 16:07:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:18] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-02 16:07:18] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:18] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-02 16:07:18] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 16:07:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-02 16:07:32] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:32] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:32] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:07:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-02 16:07:33] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:33] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-02 16:07:33] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:07:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 16:07:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 16:08:00] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 16:08:00] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 26.504406s from omnipathdb.org (604 bytes/s); Redirect: 0s, DNS look up: 0.00146s, Connection: 0.002309s, Pretransfer: 0.145261s, First byte at: 26.504256s
[2026-03-02 16:08:00] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 21:08:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 22:08:00 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
[2026-03-02 16:08:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:08:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:15] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:08:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-02 16:08:16] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-02 16:08:16] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-03-02 16:08:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:16] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-03-02 16:08:16] [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
[2026-03-02 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:08:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:08:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:08:21] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-03-02 16:08:21] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-03-02 16:08:21] [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
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:08:22] [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`
[2026-03-02 16:08:22] [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`
[2026-03-02 16:08:22] [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`
[2026-03-02 16:08:22] [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`
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-02 16:08:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 16:08:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 16:08:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 16:08:27] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 5.228818s from omnipathdb.org (3 Kb/s); Redirect: 0s, DNS look up: 0.001209s, Connection: 0.002159s, Pretransfer: 0.20286s, First byte at: 5.228668s
[2026-03-02 16:08:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 21:08:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 22:08:27 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
[2026-03-02 16:08:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-02 16:08:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:29] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:08:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-02 16:08:30] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-02 16:08:30] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-03-02 16:08:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:30] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-03-02 16:08:31] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [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`
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 16:08:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 16:08:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 16:08:32] [TRACE]   [OmnipathR] Downloaded 9.1 Kb in 0.952545s from omnipathdb.org (9.6 Kb/s); Redirect: 0s, DNS look up: 0.001365s, Connection: 0.00204s, Pretransfer: 0.144853s, First byte at: 0.952432s
[2026-03-02 16:08:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 21:08:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 22:08:32 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
[2026-03-02 16:08:33] [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`
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:33] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-02 16:08:33] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:33] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-03-02 16:08:33] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-03-02 16:08:33] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
--- finished re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2026-03-02 16:08:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:08:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-03-02 16:08:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:08:48] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:08:48] [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`
[2026-03-02 16:08:48] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-03-02 16:08:48] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-03-02 16:08:50] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 16:08:50] [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`
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-03-02 16:08:50] [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`
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-03-02 16:08:50] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-03-02 16:08:51] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.

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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted