| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4961 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4690 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 546/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.17.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: decoupleR |
| Version: 2.17.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.17.0.tar.gz |
| StartedAt: 2026-04-17 03:34:51 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 03:45:01 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 610.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.17.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2026-04-17 03:35:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:35:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:39] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:35:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 03:35:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 03:35:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 03:35:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 03:35:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 03:35:40] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 03:35:40] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 03:35:40] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.89.0(2026-04-16); AnnotationDbi 1.73.1(2026-04-16); AUCell 1.33.0(2026-04-16); backports 1.5.0(2024-05-23); beachmat 2.27.5(2026-04-16); Biobase 2.71.0(2026-04-16); BiocGenerics 0.57.0(2026-04-16); BiocParallel 1.45.0(2026-04-16); BiocSingular 1.27.1(2026-04-16); Biostrings 2.79.5(2026-04-16); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.17.0(2026-04-16); DelayedArray 0.37.1(2026-04-16); DelayedMatrixStats 1.33.0(2026-04-16); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomicRanges 1.63.2(2026-04-16); glue 1.8.0(2024-09-30); graph 1.89.1(2026-04-16); GSEABase 1.73.0(2026-04-16); GSVA 2.5.35(2026-04-16); h5mread 1.3.3(2026-04-16); HDF5Array 1.39.1(2026-04-16); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.45.0(2026-04-16); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.51.1(2026-04-16); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.23.0(2026-04-16); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); OmnipathR 3.19.12(2026-04-16); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.55.14(2026-03-09); rhdf5filters 1.23.3(2026-04-16); Rhdf5lib 1.33.0(2026-03-09); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.11.1(2026-04-16); S4Vectors 0.49.1(2026-04-16); ScaledMatrix 1.19.0(2026-04-16); Seqinfo 1.1.0(2026-04-16); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.33.2(2026-04-16); SparseArray 1.11.13(2026-04-16); sparseMatrixStats 1.23.0(2026-04-16); SpatialExperiment 1.21.0(2026-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.41.1(2026-04-16); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.51.0(2026-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2026-04-17 03:35:40] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Contains 10 files.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:35:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 03:35:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 03:35:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 03:35:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 03:35:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:35:41] [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 44.661 3.955 57.803
get_dorothea 33.106 1.742 37.741
run_fgsea 29.378 1.342 30.884
run_aucell 12.343 2.030 14.686
get_progeny 7.233 0.456 14.157
* 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:
[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
* 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
‘/home/biocbuild/bbs-3.23-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.17.0’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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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Warning: stack imbalance in '.Call', 162 then 164
[2026-04-17 03:40:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:40:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 03:40:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 03:40:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 03:40:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 03:40:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 03:40:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 03:40:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 03:40:29] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.89.0(2026-04-16); AnnotationDbi 1.73.1(2026-04-16); AUCell 1.33.0(2026-04-16); backports 1.5.0(2024-05-23); beachmat 2.27.5(2026-04-16); Biobase 2.71.0(2026-04-16); BiocGenerics 0.57.0(2026-04-16); BiocParallel 1.45.0(2026-04-16); BiocSingular 1.27.1(2026-04-16); Biostrings 2.79.5(2026-04-16); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); class 7.3-23(2025-01-01); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.17.0(2026-04-16); DelayedArray 0.37.1(2026-04-16); DelayedMatrixStats 1.33.0(2026-04-16); desc 1.4.3(2023-12-10); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.37.4(2026-04-16); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomicRanges 1.63.2(2026-04-16); ggplot2 4.0.0(2025-09-11); glue 1.8.0(2024-09-30); graph 1.89.1(2026-04-16); GSEABase 1.73.0(2026-04-16); GSVA 2.5.35(2026-04-16); gtable 0.3.6(2024-10-25); h5mread 1.3.3(2026-04-16); HDF5Array 1.39.1(2026-04-16); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.45.0(2026-04-16); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.51.1(2026-04-16); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.23.0(2026-04-16); 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 3.1-168(2025-03-31); OmnipathR 3.19.12(2026-04-16); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); plotly 4.10.4(2024-01-13); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.55.14(2026-03-09); rhdf5filters 1.23.3(2026-04-16); Rhdf5lib 1.33.0(2026-03-09); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); rpart 4.1.24(2025-01-07); RSQLite 2.3.9(2024-12-03); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.11.1(2026-04-16); S4Vectors 0.49.1(2026-04-16); S7 0.2.0(2024-11-07); ScaledMatrix 1.19.0(2026-04-16); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.1.0(2026-04-16); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.33.2(2026-04-16); SparseArray 1.11.13(2026-04-16); sparseMatrixStats 1.23.0(2026-04-16); SpatialExperiment 1.21.0(2026-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.41.1(2026-04-16); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.45.0(2026-04-16); viridisLite 0.4.2(2023-05-02); waldo 0.6.1(2024-11-07); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.51.0(2026-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2026-04-17 03:40:29] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Contains 10 files.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 03:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 03:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 03:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 03:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-04-17 03:40:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:40:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:31] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-04-17 03:40:31] [INFO] [OmnipathR] Cache record does not exist: `db://organisms`
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Loading database `organisms` from source.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:31] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:31] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-04-17 03:40:31] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-04-17 03:40:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:40:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-04-17 03:40:31] [TRACE] [OmnipathR] Sending HTTP request.
[2026-04-17 03:40:32] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-04-17 03:40:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:40:32] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.818818s from rescued.omnipathdb.org (48.7 Kb/s); Redirect: 0s, DNS look up: 0.000753s, Connection: 0.163475s, Pretransfer: 0.330286s, First byte at: 0.655932s
[2026-04-17 03:40:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:40:39 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, 17 Apr 2026 04:40:39 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-04-17 03:40:32] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 17 Apr 2026 03:40:39 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, 17 Apr 2026 04:40:39 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-04-17 03:40:34] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:34] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-17 03:40:34] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:40:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-17 03:40:35] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-04-17 03:40:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-04-17 03:40:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:40:35] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:40:35] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-17 03:40:35] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 0.190997s from omabrowser.org (66 Kb/s); Redirect: 0s, DNS look up: 0.008119s, Connection: 0.010251s, Pretransfer: 0.025972s, First byte at: 0.190543s
[2026-04-17 03:40:35] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 17 Apr 2026 03:40:42 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=dk3xWYSoMdg3ofLjs%2BUoA9CkoRLlphQ8AcOiRd%2FxMAEpzxa5H8D0A%2BLEb76adjcUXF8cOcHDHnM9XP8YGu%2BqNP%2BoNFE%2FJbA7UKYjerzt0hpQTw%2F75so%2BIGpL5Xd%2BPesM1A%3D%3D"}]}; cf-ray: 9ed868ee2ee3ce59-SIN; alt-svc: h3=":443"; ma=86400
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-17 03:40:37] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:37] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-17 03:40:37] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:40:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-17 03:40:37] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-17 03:40:37] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-17 03:41:21] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:21] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:21] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:41:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-17 03:41:22] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:22] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-04-17 03:41:22] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2026-04-17 03:41:22] [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]
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:41:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:41:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:23] [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)]
[2026-04-17 03:41:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:41:24] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:41:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:41:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.681514s from omnipathdb.org (23 Kb/s); Redirect: 0s, DNS look up: 0.006534s, Connection: 0.172985s, Pretransfer: 0.343381s, First byte at: 0.681064s
[2026-04-17 03:41:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:41:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:41:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:41:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:26] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-17 03:41:26] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:26] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2026-04-17 03:41:26] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-04-17 03:41:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:41:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-17 03:41:27] [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]
[2026-04-17 03:41:27] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:41:27] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:29] [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)]
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:41:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:41:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.667241s from omnipathdb.org (23.5 Kb/s); Redirect: 0s, DNS look up: 0.000797s, Connection: 0.166144s, Pretransfer: 0.335766s, First byte at: 0.666835s
[2026-04-17 03:41:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:41:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:41:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:41:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:38] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:41:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-17 03:41:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-17 03:41:41] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-04-17 03:41:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:41] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-04-17 03:41:41] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2026-04-17 03:41:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:41:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:44] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:41:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-17 03:41:44] [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]
[2026-04-17 03:41:44] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:41:44] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:41:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:41:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:45] [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)]
[2026-04-17 03:41:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-17 03:41:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-17 03:41:47] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2026-04-17 03:41:50] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Checking on-disk cache for database `oma`.
[2026-04-17 03:41:50] [INFO] [OmnipathR] Cache record does not exist: `db://oma`
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Loading database `oma` from source.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-17 03:41:50] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:41:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:41:50] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-17 03:41:50] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-17 03:41:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-17 03:41:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:41:50] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:42:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-17 03:42:02] [TRACE] [OmnipathR] Downloaded 12.7 Kb in 11.346828s from omabrowser.org (1.1 Kb/s); Redirect: 0s, DNS look up: 0.001641s, Connection: 0.004734s, Pretransfer: 0.020781s, First byte at: 11.34662s
[2026-04-17 03:42:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 17 Apr 2026 03:42:09 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_2026-04-17_034208.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=a8766b76cc3f9926; expires=Sun, 16-Apr-2028 03:42:09 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=LAOUPsdvXgNCaf18vGYSCCM1sgTJMgaMJWleZ8hb2285PucjLIXB5vNMSpZzfcokFsza2AH78iujZfDbE3lwmN5BKQT7E%2BYGOx3I7JAbfLIbyZP2w7RYaDA8QiIEriGkGg%3D%3D"}]}; cf-ray: 9ed86ac68ad49db9-SIN; alt-svc: h3=":443"; ma=86400
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-17 03:42:04] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:04] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:04] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-17 03:42:04] [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`
[2026-04-17 03:42:04] [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`.
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:04] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-17 03:42:04] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-17 03:42:04] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-17 03:42:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:42:04] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:42:05] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-17 03:42:05] [TRACE] [OmnipathR] Downloaded 31 bytes in 1.011786s from rest.uniprot.org (30 bytes/s); Redirect: 0s, DNS look up: 0.074814s, Connection: 0.237054s, Pretransfer: 0.564455s, First byte at: 1.011645s
[2026-04-17 03:42:05] [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: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 17 Apr 2026 03:42:13 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
[2026-04-17 03:42:16] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-17 03:42:16] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2026-04-17 03:42:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:16] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:16] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2026-04-17 03:42:17] [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`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-17 03:42:17] [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`
[2026-04-17 03:42:17] [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`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:17] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-17 03:42:17] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-17 03:42:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:42:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:42:18] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-17 03:42:18] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.862771s from rest.uniprot.org (35 bytes/s); Redirect: 0s, DNS look up: 0.000745s, Connection: 0.162962s, Pretransfer: 0.487492s, First byte at: 0.862632s
[2026-04-17 03:42:18] [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: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 17 Apr 2026 03:42:25 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
[2026-04-17 03:42:25] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-17 03:42:25] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2026-04-17 03:42:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:25] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:25] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2026-04-17 03:42:26] [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`.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Saving database `oma` to on-disk cache.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:26] [INFO] [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-04-17 03:42:26] [INFO] [OmnipathR] Download ready [key=e0bb78c15459541ddf64018acdc4bad95c1fa369, version=1]
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:26] [INFO] [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:26] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-04-17 03:42:26] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-04-17 03:42:27] [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`.
[2026-04-17 03:42:27] [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`
[2026-04-17 03:42:27] [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`.
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:27] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-04-17 03:42:27] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-17 03:42:27] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-17 03:42:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:42:27] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:42:28] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-04-17 03:42:28] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.966364s from rest.uniprot.org (44 bytes/s); Redirect: 0s, DNS look up: 0.07756s, Connection: 0.241355s, Pretransfer: 0.572493s, First byte at: 0.966215s
[2026-04-17 03:42:28] [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: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 17 Apr 2026 03:42:35 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
[2026-04-17 03:42:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-04-17 03:42:35] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2026-04-17 03:42:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:35] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:35] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-04-17 03:42:35] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-17 03:42:35] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-17 03:42:35] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-04-17 03:42:35] [TRACE] [OmnipathR] 163601 rows before translation, 12830 uniprot IDs in column `uniprot`.
[2026-04-17 03:42:36] [TRACE] [OmnipathR] 163601 rows after translation; translated 12830 `uniprot` IDs in column `uniprot` to 12748 `genesymbol` IDs in column `genesymbol`.
[2026-04-17 03:42:36] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:42:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-04-17 03:42:36] [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]
[2026-04-17 03:42:36] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:42:36] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:42:36] [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)]
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [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`
[2026-04-17 03:42:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:42:36] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:42:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:42:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.65991s from omnipathdb.org (23.8 Kb/s); Redirect: 0s, DNS look up: 0.00079s, Connection: 0.1643s, Pretransfer: 0.332313s, First byte at: 0.659482s
[2026-04-17 03:42:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:42:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:42:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:42:41] [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`
[2026-04-17 03:42:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:41] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:42:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-17 03:42:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-17 03:42:42] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2026-04-17 03:42:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:42:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:42:42] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2026-04-17 03:42:57] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2026-04-17 03:43:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:43:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2026-04-17 03:43:14] [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]
[2026-04-17 03:43:14] [TRACE] [OmnipathR] Organism(s): 10090
[2026-04-17 03:43:14] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:43:14] [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)]
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [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`
[2026-04-17 03:43:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:43:14] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:43:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:43:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.660088s from omnipathdb.org (23.8 Kb/s); Redirect: 0s, DNS look up: 0.000841s, Connection: 0.163478s, Pretransfer: 0.330939s, First byte at: 0.659657s
[2026-04-17 03:43:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:43:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:43:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:43:21] [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`
[2026-04-17 03:43:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:21] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:43:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-17 03:43:22] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-17 03:43:23] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2026-04-17 03:43:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:23] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2026-04-17 03:43:36] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-17 03:43:51] [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]
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:43:51] [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)]
[2026-04-17 03:43:51] [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`
[2026-04-17 03:43:51] [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`
[2026-04-17 03:43:51] [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`
[2026-04-17 03:43:51] [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`
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-17 03:43:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-17 03:43:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-17 03:43:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:43:51] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:43:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:43:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.685521s from omnipathdb.org (22.9 Kb/s); Redirect: 0s, DNS look up: 0.000839s, Connection: 0.165707s, Pretransfer: 0.355039s, First byte at: 0.68502s
[2026-04-17 03:43:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:43:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:43:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:43:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-17 03:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:54] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:43:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-17 03:43:55] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-17 03:43:55] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-04-17 03:43:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:43:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:43:55] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-04-17 03:43:59] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-04-17 03:43:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:43:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-17 03:43:59] [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]
[2026-04-17 03:43:59] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:43:59] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:43:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:44:00] [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)]
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [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`
[2026-04-17 03:44:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-17 03:44:00] [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=TRUE,ssl_verifyhost=TRUE]
[2026-04-17 03:44:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-04-17 03:44:00] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.504739s from omnipathdb.org (13.3 Kb/s); Redirect: 0s, DNS look up: 0.000754s, Connection: 0.166485s, Pretransfer: 0.336478s, First byte at: 0.504437s
[2026-04-17 03:44:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 17 Apr 2026 03:44:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 17 Apr 2026 04:44:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-17 03:44:03] [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`
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:44:03] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-17 03:44:03] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 03:44:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:44:03] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-17 03:44:03] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-17 03:44:04] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2026-04-17 03:44:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:44:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-17 03:44:04] [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]
[2026-04-17 03:44:05] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:44:05] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:44:05] [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)]
[2026-04-17 03:44:05] [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`
[2026-04-17 03:44:05] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-17 03:44:05] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-17 03:44:08] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-04-17 03:44:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-04-17 03:44:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-17 03:44:09] [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]
[2026-04-17 03:44:09] [TRACE] [OmnipathR] Organism(s): 9606
[2026-04-17 03:44:09] [TRACE] [OmnipathR] Orthology targets:
[2026-04-17 03:44:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-17 03:44:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 03:44:10] [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)]
[2026-04-17 03:44:10] [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`
[2026-04-17 03:44:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-17 03:44:10] [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`
[2026-04-17 03:44:10] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-17 03:44:10] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-17 03:44:10] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-17 03:44:11] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
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 ─────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).
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 | 0.096 | 0.016 | 0.113 | |
| convert_f_defaults | 0.063 | 0.000 | 0.064 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.03 | 0.00 | 0.03 | |
| extract_sets | 0.03 | 0.00 | 0.03 | |
| filt_minsize | 0.056 | 0.000 | 0.056 | |
| get_collectri | 44.661 | 3.955 | 57.803 | |
| get_dorothea | 33.106 | 1.742 | 37.741 | |
| get_profile_of | 0.000 | 0.000 | 0.001 | |
| get_progeny | 7.233 | 0.456 | 14.157 | |
| get_resource | 1.272 | 0.096 | 3.871 | |
| get_toy_data | 0.003 | 0.000 | 0.004 | |
| intersect_regulons | 0.035 | 0.004 | 0.039 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.045 | 0.011 | 0.057 | |
| run_aucell | 12.343 | 2.030 | 14.686 | |
| run_consensus | 2.846 | 0.368 | 3.263 | |
| run_fgsea | 29.378 | 1.342 | 30.884 | |
| run_gsva | 2.600 | 0.556 | 3.236 | |
| run_mdt | 0.204 | 0.049 | 0.254 | |
| run_mlm | 0.120 | 0.024 | 0.147 | |
| run_ora | 0.713 | 0.052 | 0.779 | |
| run_udt | 0.494 | 0.032 | 0.533 | |
| run_ulm | 0.098 | 0.016 | 0.117 | |
| run_viper | 1.114 | 0.229 | 1.381 | |
| run_wmean | 1.151 | 0.084 | 1.255 | |
| run_wsum | 1.096 | 0.076 | 1.192 | |
| show_methods | 0.125 | 0.004 | 0.130 | |
| show_resources | 0.105 | 0.008 | 1.038 | |
| tidyeval | 0 | 0 | 0 | |