| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-22 11:36 -0400 (Fri, 22 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4936 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4621 |
| 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 | ||||
| Package 542/2378 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.19.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | ||||||||||
| See other builds for decoupleR in R Universe. | ||||||||||||||
|
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. |
| Package: decoupleR |
| Version: 2.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.19.0.tar.gz |
| StartedAt: 2026-05-21 19:07:11 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 19:11:03 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 231.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/decoupleR.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-21 23:07:12 UTC
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:07:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-21 19:07:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-21
[2026-05-21 19:07:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-21 19:05:36 UTC; unix
[2026-05-21 19:07:26] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-21 19:07:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-21 19:07:26] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-21; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-21 19:07:26] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-21 19:07:26] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.91.0(2026-05-21); AnnotationDbi 1.75.0(2026-05-21); AUCell 1.35.0(2026-05-21); backports 1.5.1(2026-04-03); beachmat 2.29.0(2026-05-21); Biobase 2.73.1(2026-05-21); BiocGenerics 0.59.2(2026-05-21); BiocParallel 1.47.0(2026-05-21); BiocSingular 1.29.0(2026-05-21); Biostrings 2.81.1(2026-05-21); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); 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 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); data.table 1.18.4(2026-05-06); DBI 1.3.0(2026-02-25); decoupleR 2.19.0(2026-05-21); DelayedArray 0.39.2(2026-05-21); DelayedMatrixStats 1.35.0(2026-05-21); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicRanges 1.65.0(2026-05-21); glue 1.8.1(2026-04-17); graph 1.91.0(2026-05-21); GSEABase 1.75.0(2026-05-21); GSVA 2.7.2(2026-05-21); h5mread 1.5.0(2026-05-21); HDF5Array 1.41.0(2026-05-21); 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 2.3.1(2026-05-04); IRanges 2.47.1(2026-05-21); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.53.0(2026-05-21); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.5(2026-04-04); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.25.0(2026-05-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); OmnipathR 4.1.0(2026-05-21); otel 0.2.0(2025-08-29); parallelly 1.47.0(2026-04-17); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.2(2026-04-10); 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); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rhdf5 2.57.0(2026-05-21); rhdf5filters 1.25.0(2026-05-21); Rhdf5lib 2.1.0(2026-05-21); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.13.0(2026-05-21); S4Vectors 0.51.2(2026-05-21); ScaledMatrix 1.21.0(2026-05-21); Seqinfo 1.3.0(2026-05-21); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.35.1(2026-05-21); SparseArray 1.13.2(2026-05-21); sparseMatrixStats 1.25.0(2026-05-21); SpatialExperiment 1.23.0(2026-05-21); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.43.0(2026-05-21); 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); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.53.0(2026-05-21); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-21 19:07:26] [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
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`.
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-21 19:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:07:26] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_collectri 10.160 1.224 18.449
run_fgsea 9.864 0.283 10.222
get_dorothea 8.312 0.610 11.706
get_progeny 2.653 0.202 9.641
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[3] 0.519 - 0.548 [3]
[4] 0.519 - 0.548 [4]
[5] 0.010 | 0.010 [5]
[6] 0.010 | 0.010 [6]
[7] 0.087 - 0.076 [7]
[8] 0.087 - 0.076 [8]
[9] 1.000 - 0.977 [9]
[10] 1.000 - 0.977 [10]
... ... ... and 134 more ...
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
Error:
! Test failures.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.24-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.19.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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[2026-05-21 19:09:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:04] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:09:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-21 19:09:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-21
[2026-05-21 19:09:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-05-21 19:05:36 UTC; unix
[2026-05-21 19:09:04] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-21 19:09:04] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-21 19:09:04] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 Patched (2026-05-01 r89994); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-05-21; pandoc=3.9.0.2 @ /usr/local/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-05-21 19:09:04] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.56; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.8.3; deflate=1.25; zstd=1.5.7; PCRE=10.47 2025-10-21; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-05-21 19:09:05] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.91.0(2026-05-21); AnnotationDbi 1.75.0(2026-05-21); AUCell 1.35.0(2026-05-21); backports 1.5.1(2026-04-03); beachmat 2.29.0(2026-05-21); Biobase 2.73.1(2026-05-21); BiocGenerics 0.59.2(2026-05-21); BiocParallel 1.47.0(2026-05-21); BiocSingular 1.29.0(2026-05-21); Biostrings 2.81.1(2026-05-21); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); broom 1.0.13(2026-05-14); 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); class 7.3-23(2025-01-01); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); data.table 1.18.4(2026-05-06); DBI 1.3.0(2026-02-25); decoupleR 2.19.0(2026-05-21); DelayedArray 0.39.2(2026-05-21); DelayedMatrixStats 1.35.0(2026-05-21); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); e1071 1.7-17(2025-12-18); 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 1.39.0(2026-05-21); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicRanges 1.65.0(2026-05-21); ggplot2 4.0.3(2026-04-22); glue 1.8.1(2026-04-17); graph 1.91.0(2026-05-21); GSEABase 1.75.0(2026-05-21); GSVA 2.7.2(2026-05-21); gtable 0.3.6(2024-10-25); h5mread 1.5.0(2026-05-21); HDF5Array 1.41.0(2026-05-21); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); IRanges 2.47.1(2026-05-21); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.53.0(2026-05-21); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lazyeval 0.2.3(2026-04-04); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.5(2026-04-04); MASS 7.3-65(2025-02-28); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.25.0(2026-05-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); mixtools 2.0.0.1(2025-03-08); nlme 3.1-169(2026-03-27); OmnipathR 4.1.0(2026-05-21); otel 0.2.0(2025-08-29); parallelly 1.47.0(2026-04-17); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); proxy 0.4-29(2025-12-29); purrr 1.2.2(2026-04-10); 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); ranger 0.18.0(2026-01-16); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rhdf5 2.57.0(2026-05-21); rhdf5filters 1.25.0(2026-05-21); Rhdf5lib 2.1.0(2026-05-21); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); rpart 4.1.27(2026-03-27); RSQLite 3.52.0(2026-05-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.13.0(2026-05-21); S4Vectors 0.51.2(2026-05-21); S7 0.2.2(2026-04-22); ScaledMatrix 1.21.0(2026-05-21); scales 1.4.0(2025-04-24); segmented 2.2-1(2026-01-29); Seqinfo 1.3.0(2026-05-21); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.35.1(2026-05-21); SparseArray 1.13.2(2026-05-21); sparseMatrixStats 1.25.0(2026-05-21); SpatialExperiment 1.23.0(2026-05-21); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.43.0(2026-05-21); survival 3.8-6(2026-01-16); testthat 3.3.2(2026-01-11); 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); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); viper 1.47.0(2026-05-21); viridisLite 0.4.3(2026-02-04); waldo 0.6.2(2025-07-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.53.0(2026-05-21); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-21 19:09:05] [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
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Contains 10 files.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Pandoc version: `3.9.0.2`.
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:06] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-05-21 19:09:06] [INFO] [OmnipathR] Cache record does not exist: `db://organisms`
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Loading database `organisms` from source.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:06] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:06] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-21 19:09:06] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-21 19:09:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-21 19:09:06] [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]
[2026-05-21 19:09:06] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-21 19:09:06] [TRACE] [OmnipathR] Sending HTTP request.
[2026-05-21 19:09:07] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-05-21 19:09:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:09:07] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.621881s from rescued.omnipathdb.org (64.1 Kb/s); Redirect: 0s, DNS look up: 0.001485s, Connection: 0.002431s, Pretransfer: 0.321357s, First byte at: 0.47433s
[2026-05-21 19:09:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:09:07 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: Fri, 22 May 2026 00:09:07 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-21 19:09:07] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Thu, 21 May 2026 23:09:07 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=Fri, 22 May 2026 00:09:07 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-21 19:09:07] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-21 19:09:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:07] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-21 19:09:07] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-21 19:09:08] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-21 19:09:08] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-21 19:09:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:09:08] [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]
[2026-05-21 19:09:08] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-05-21 19:09:08] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.166724s from omabrowser.org (16 Kb/s); Redirect: 0s, DNS look up: 0.008945s, Connection: 0.02279s, Pretransfer: 0.041506s, First byte at: 0.166589s
[2026-05-21 19:09:08] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 21 May 2026 23:09:08 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=Qw%2Bn%2F%2FC2FtyhNpgdzBbpDB4q%2B%2FtYkT8pQBpre0SHAw9Tdln9Ax%2FtuVbNqlcXYAsu8IJ5T5ckxq%2BAlizqFz47HdOmfB1hJjsGdIQ9SwIWjakqx0B5KylJXgKQJ92BI0nFgg%3D%3D"}]}; cf-ray: 9ff73f3dbc701759-IAD; alt-svc: h3=":443"; ma=86400
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-21 19:09:09] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:09] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-21 19:09:09] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:09] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-21 19:09:09] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-21 19:09:09] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-21 19:09:21] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:21] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:21] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:21] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-05-21 19:09:22] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:22] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:22] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=TFcensus,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=TFcensus,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:09:23] [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]
[2026-05-21 19:09:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.311904s from omnipathdb.org (50.3 Kb/s); Redirect: 0s, DNS look up: 0.001073s, Connection: 0.002073s, Pretransfer: 0.154534s, First byte at: 0.311724s
[2026-05-21 19:09:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:09:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:09:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:09:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:23] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-05-21 19:09:23] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:23] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:23] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-05-21 19:09:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=PROGENy,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:09:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=PROGENy,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:09:25] [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]
[2026-05-21 19:09:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:09:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.293559s from omnipathdb.org (53.5 Kb/s); Redirect: 0s, DNS look up: 0.001883s, Connection: 0.002926s, Pretransfer: 0.146597s, First byte at: 0.293402s
[2026-05-21 19:09:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:09:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:09:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:09:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:31] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:31] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-05-21 19:09:33] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-05-21 19:09:33] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-05-21 19:09:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:33] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:33] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2026-05-21 19:09:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=PROGENy,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:09:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=PROGENy,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:09:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:36] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-05-21 19:09:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-05-21 19:09:36] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2026-05-21 19:09:37] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Checking on-disk cache for database `oma`.
[2026-05-21 19:09:37] [INFO] [OmnipathR] Cache record does not exist: `db://oma`
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Loading database `oma` from source.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-05-21 19:09:37] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:37] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-05-21 19:09:37] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-05-21 19:09:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-05-21 19:09:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:09:37] [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]
[2026-05-21 19:09:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-05-21 19:09:48] [TRACE] [OmnipathR] Downloaded 8 Kb in 11.128247s from omabrowser.org (736 bytes/s); Redirect: 0s, DNS look up: 0.001838s, Connection: 0.014381s, Pretransfer: 0.032744s, First byte at: 11.12801s
[2026-05-21 19:09:48] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 21 May 2026 23:09:48 GMT; content-type: text/tsv; charset=utf-8; content-length: 1187278; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2026-05-21_230948.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=1a5495fd28391a38; expires=Sat, 20-May-2028 23:09:48 UTC; Path=/; cf-cache-status: DYNAMIC; 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=utRRVv4K0TFDssNRM0OR6dOKfi6RANfdtshXZTlTRVXcm1ajUeUKNh9Fep20WnxpxgCD2lIkQiWAHrntrofSjFmPLQMzAr2MNsgEHYf1YcmR04hX47ssSap3uDm8Tuc3uQ%3D%3D"}]}; cf-ray: 9ff73ff77f79d650-IAD; alt-svc: h3=":443"; ma=86400
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-05-21 19:09:51] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:51] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2026-05-21 19:09:51] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-21 19:09:51] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:09:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:09:51] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-05-21 19:09:51] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-21 19:09:51] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-21 19:09:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:09:51] [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]
[2026-05-21 19:09:52] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-05-21 19:09:52] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.872425s from rest.uniprot.org (35 bytes/s); Redirect: 0s, DNS look up: 0.004636s, Connection: 0.005617s, Pretransfer: 0.504193s, First byte at: 0.872319s
[2026-05-21 19:09:52] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 21 May 2026 23:09:52 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-05-21 19:10:01] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:01] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:01] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] 13774 rows after translation; translated 13523 `uniprot_entry` IDs in column `id_organism_a` to 13523 `uniprot` IDs in column `id_organism_a`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-05-21 19:10:01] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:01] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-05-21 19:10:01] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:01] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:01] [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]
[2026-05-21 19:10:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-05-21 19:10:02] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.776806s from rest.uniprot.org (39 bytes/s); Redirect: 0s, DNS look up: 0.001632s, Connection: 0.002666s, Pretransfer: 0.489003s, First byte at: 0.77671s
[2026-05-21 19:10:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 21 May 2026 23:10:02 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-05-21 19:10:08] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:08] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] 13774 rows after translation; translated 13226 `uniprot_entry` IDs in column `id_organism_b` to 13226 `uniprot` IDs in column `id_organism_b`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Saving database `oma` to on-disk cache.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [INFO] [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-05-21 19:10:08] [INFO] [OmnipathR] Download ready [key=e0bb78c15459541ddf64018acdc4bad95c1fa369, version=1]
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [INFO] [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:08] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-05-21 19:10:08] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:08] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-05-21 19:10:08] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-05-21 19:10:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:08] [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]
[2026-05-21 19:10:09] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-05-21 19:10:09] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.529787s from rest.uniprot.org (81 bytes/s); Redirect: 0s, DNS look up: 0.001769s, Connection: 0.002694s, Pretransfer: 0.246686s, First byte at: 0.529695s
[2026-05-21 19:10:09] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 21 May 2026 23:10:09 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-05-21 19:10:14] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-05-21 19:10:14] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2026-05-21 19:10:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:14] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:14] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] 163601 rows before translation, 12830 uniprot IDs in column `uniprot`.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] 163601 rows after translation; translated 12830 `uniprot` IDs in column `uniprot` to 12748 `genesymbol` IDs in column `genesymbol`.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C,D],organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:15] [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]
[2026-05-21 19:10:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:10:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.45467s from omnipathdb.org (34.5 Kb/s); Redirect: 0s, DNS look up: 0.001741s, Connection: 0.00268s, Pretransfer: 0.298491s, First byte at: 0.454478s
[2026-05-21 19:10:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:10:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:10:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:10:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:18] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-05-21 19:10:19] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-05-21 19:10:19] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2026-05-21 19:10:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:19] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:22] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Organism(s): 10090
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C,D],organisms=10090,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:26] [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]
[2026-05-21 19:10:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:10:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.297911s from omnipathdb.org (52.7 Kb/s); Redirect: 0s, DNS look up: 0.001485s, Connection: 0.002679s, Pretransfer: 0.151919s, First byte at: 0.297736s
[2026-05-21 19:10:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:10:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:10:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:10:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-21 19:10:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:29] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:29] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-05-21 19:10:29] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-05-21 19:10:29] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2026-05-21 19:10:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:30] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:32] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,loops=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:36] [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`
[2026-05-21 19:10:36] [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`
[2026-05-21 19:10:36] [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`
[2026-05-21 19:10:36] [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`
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:36] [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]
[2026-05-21 19:10:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:10:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.447896s from omnipathdb.org (35.1 Kb/s); Redirect: 0s, DNS look up: 0.001784s, Connection: 0.002856s, Pretransfer: 0.297382s, First byte at: 0.447715s
[2026-05-21 19:10:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:10:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:10:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:10:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:39] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:39] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-05-21 19:10:39] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-05-21 19:10:39] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-05-21 19:10:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:39] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:40] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=[evidences,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [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`
[2026-05-21 19:10:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-21 19:10:40] [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]
[2026-05-21 19:10:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.231879s from omnipathdb.org (29 Kb/s); Redirect: 0s, DNS look up: 0.001683s, Connection: 0.002442s, Pretransfer: 0.153996s, First byte at: 0.23175s
[2026-05-21 19:10:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 21 May 2026 23:10:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 22 May 2026 00:10:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-21 19:10:41] [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`
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:41] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-05-21 19:10:41] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-21 19:10:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:41] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-05-21 19:10:41] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,loops=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-05-21 19:10:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-05-21 19:10:42] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE]
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Organism(s): 9606
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Orthology targets:
[2026-05-21 19:10:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-21 19:10:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-21 19:10:43] [TRACE] [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=[evidences,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-05-21 19:10:43] [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`
[2026-05-21 19:10:43] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-05-21 19:10:43] [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`
[2026-05-21 19:10:43] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-05-21 19:10:43] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-05-21 19:10:43] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-05-21 19:10:43] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Saving _problems/test-statistic-fgsea-26.R
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
Expected `res_1` to equal `exp_1`.
Differences:
actual vs expected
p_value
- actual[1, ] 0.104845953
+ expected[1, ] 0.075479709
- actual[2, ] 0.104845953
+ expected[2, ] 0.075479709
- actual[3, ] 0.519279295
+ expected[3, ] 0.548454870
- actual[4, ] 0.519279295
+ expected[4, ] 0.548454870
actual[5, ] 0.010000000
actual[6, ] 0.010000000
- actual[7, ] 0.086660121
+ expected[7, ] 0.076411558
- actual[8, ] 0.086660121
+ expected[8, ] 0.076411558
- actual[9, ] 1.000000000
+ expected[9, ] 0.976649086
- actual[10, ] 1.000000000
+ expected[10, ] 0.976649086
and 134 more ...
actual$p_value | expected$p_value
[1] 0.105 - 0.075 [1]
[2] 0.105 - 0.075 [2]
[3] 0.519 - 0.548 [3]
[4] 0.519 - 0.548 [4]
[5] 0.010 | 0.010 [5]
[6] 0.010 | 0.010 [6]
[7] 0.087 - 0.076 [7]
[8] 0.087 - 0.076 [8]
[9] 1.000 - 0.977 [9]
[10] 1.000 - 0.977 [10]
... ... ... and 134 more ...
[ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
Error:
! Test failures.
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.031 | 0.003 | 0.035 | |
| convert_f_defaults | 0.009 | 0.000 | 0.009 | |
| decouple | 0.001 | 0.000 | 0.000 | |
| dot-fit_preprocessing | 0.008 | 0.001 | 0.010 | |
| extract_sets | 0.007 | 0.001 | 0.008 | |
| filt_minsize | 0.013 | 0.000 | 0.013 | |
| get_collectri | 10.160 | 1.224 | 18.449 | |
| get_dorothea | 8.312 | 0.610 | 11.706 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 2.653 | 0.202 | 9.641 | |
| get_resource | 0.378 | 0.079 | 2.510 | |
| get_toy_data | 0.001 | 0.000 | 0.001 | |
| intersect_regulons | 0.010 | 0.004 | 0.014 | |
| pipe | 0.000 | 0.001 | 0.000 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.012 | 0.003 | 0.015 | |
| run_aucell | 3.397 | 0.971 | 4.376 | |
| run_consensus | 0.599 | 0.122 | 0.716 | |
| run_fgsea | 9.864 | 0.283 | 10.222 | |
| run_gsva | 0.767 | 0.270 | 1.035 | |
| run_mdt | 0.049 | 0.016 | 0.065 | |
| run_mlm | 0.035 | 0.009 | 0.042 | |
| run_ora | 0.150 | 0.020 | 0.169 | |
| run_udt | 0.098 | 0.020 | 0.117 | |
| run_ulm | 0.024 | 0.004 | 0.028 | |
| run_viper | 0.327 | 0.119 | 0.443 | |
| run_wmean | 0.213 | 0.027 | 0.239 | |
| run_wsum | 0.227 | 0.027 | 0.252 | |
| show_methods | 0.018 | 0.003 | 0.020 | |
| show_resources | 0.023 | 0.007 | 0.753 | |
| tidyeval | 0.001 | 0.000 | 0.000 | |