Build/check report for BioC 3.23 - BUILD results for decoupleR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4013
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: 2025-11-12 16:06:22 -0500 (Wed, 12 Nov 2025)
EndedAt: 2025-11-12 16:08:00 -0500 (Wed, 12 Nov 2025)
EllapsedTime: 98.1 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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

Quitting from decoupleR.Rmd:31-46 [vignette_setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `citation()`:
! there is no package called 'GSVA'
---
Backtrace:
    ▆
 1. └─utils::citation("GSVA")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'decoupleR.Rmd' failed with diagnostics:
there is no package called 'GSVA'
--- failed re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2025-11-12 16:06:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-12
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-12 20:19:41 UTC; unix
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-12 16:06:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-12 16:06:28] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-12; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-12 16:06:28] [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=1.2.11; 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=70.2; 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]
[2025-11-12 16:06:28] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.45.0(2025-11-12); BiocStyle 2.39.0(2025-11-12); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); decoupleR 2.17.0(2025-11-12); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.19.0(2025-11-12); otel 0.2.0(2025-08-29); parallelly 1.45.1(2025-07-24); 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 1.2.0(2025-11-04); 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 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); 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 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-12 16:06:28] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-11-12 16:06:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:29] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:29] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-12 16:06:29] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-12 16:06:29] [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]
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-12 16:06:29] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Downloaded 31.3 Kb in 22.407003s from www.ensembl.org (1.4 Kb/s); Redirect: 13.265962s, DNS look up: 0.007958s, Connection: 0.010559s, Pretransfer: 0.676639s, First byte at: 22.379598s
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Wed, 12 Nov 2025 21:06:29 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk; HTTP/2 302 ; date: Wed, 12 Nov 2025 21:06:42 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-94.us-east-2.compute.internal; HTTP/2 200 ; date: Wed, 12 Nov 2025 21:06:51 GMT; content-type: text/html; charset=utf-8; content-length: 32080; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Thu, 13 Nov 2025 21:02:01 GMT; set-cookie: ENSEMBL_WWW_SESSION=196992ac72d2cdd30d37acd569640fca0268a2bf8879186a560601f3; 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=Thu, 13 Nov 2025 21:02:01 GMT; set-cookie: ENSEMBL_WWW_SESSION=196992ac72d2cdd30d37acd569640fca0268a2bf8879186a560601f3; 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: ip-10-25-25-94.us-east-2.compute.internal
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Response headers: [date=Wed, 12 Nov 2025 21:06:51 GMT,content-type=text/html; charset=utf-8,content-length=32080,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Thu, 13 Nov 2025 21:02:01 GMT,set-cookie=ENSEMBL_WWW_SESSION=196992ac72d2cdd30d37acd569640fca0268a2bf8879186a560601f3; 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=Thu, 13 Nov 2025 21:02:01 GMT,set-cookie=ENSEMBL_WWW_SESSION=196992ac72d2cdd30d37acd569640fca0268a2bf8879186a560601f3; 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=ip-10-25-25-94.us-east-2.compute.internal]
[2025-11-12 16:06:51] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:51] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-12 16:06:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-12 16:06:52] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-12 16:06:52] [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]
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.490336s from omabrowser.org (17.7 Kb/s); Redirect: 0s, DNS look up: 0.040106s, Connection: 0.041025s, Pretransfer: 0.402567s, First byte at: 0.490151s
[2025-11-12 16:06:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 12 Nov 2025 21:06:52 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
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-12 16:06:53] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-12 16:06:53] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:06:53] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-12 16:06:53] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-12 16:06:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-12 16:07:07] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:07] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-12 16:07:07] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-12 16:07:08] [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]
[2025-11-12 16:07:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-12 16:07:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.467597s from omnipathdb.org (33.5 Kb/s); Redirect: 0s, DNS look up: 0.000783s, Connection: 0.001656s, Pretransfer: 0.316959s, First byte at: 0.467391s
[2025-11-12 16:07:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 12 Nov 2025 21:07:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 12 Nov 2025 22:07:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-12 16:07:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:16] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-11-12 16:07:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-12 16:07:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-12 16:07:17] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-11-12 16:07:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:17] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-11-12 16:07:17] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
2025-11-12 16:07:19.334 R[83866:1963940] XType: Using static font registry.
Warning: ggrepel: 441 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2025-11-12 16:07:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:29] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-12 16:07:29] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-12 16:07:29] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.

  |                                                                                                                    
  |                                                                                                              |   0%
  |                                                                                                                    
  |==============================================================================================================| 100%
--- finished re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:34] [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`
[2025-11-12 16:07:34] [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`
[2025-11-12 16:07:34] [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`
[2025-11-12 16:07:34] [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`
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-12 16:07:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-12 16:07:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-12 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]
[2025-11-12 16:07:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-12 16:07:35] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.291893s from omnipathdb.org (53.7 Kb/s); Redirect: 0s, DNS look up: 0.000839s, Connection: 0.001694s, Pretransfer: 0.146685s, First byte at: 0.290905s
[2025-11-12 16:07:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 12 Nov 2025 21:07:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 12 Nov 2025 22:07:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-12 16:07:37] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:37] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-12 16:07:37] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:37] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-11-12 16:07:38] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2025-11-12 16:07:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-12 16:07:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:38] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-12 16:07:39] [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]
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Downloaded 9 Kb in 0.222044s from omnipathdb.org (40.7 Kb/s); Redirect: 0s, DNS look up: 0.001109s, Connection: 0.003426s, Pretransfer: 0.149061s, First byte at: 0.221833s
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 12 Nov 2025 21:07:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 12 Nov 2025 22:07:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-12 16:07:39] [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`
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:39] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-12 16:07:39] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:39] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-12 16:07:39] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-12 16:07:40] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
Warning: ggrepel: 754 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2025-11-12 16:07:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-12 16:07:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:52] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:52] [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`
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-12 16:07:53] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-12 16:07:53] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-12 16:07:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-12 16:07:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-12 16:07:54] [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`
[2025-11-12 16:07:54] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-12 16:07:54] [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`
[2025-11-12 16:07:54] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-12 16:07:54] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-12 16:07:54] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-12 16:07:54] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.

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--- finished re-building ‘tf_sc.Rmd’

SUMMARY: processing the following file failed:
  ‘decoupleR.Rmd’

Error: Vignette re-building failed.
Execution halted