Pau Badia-i-Mompel
| Snapshot Date: 2025-11-04 13:45 -0500 (Tue, 04 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: RELEASE_3_22 |
| git_last_commit: ff3aa1d |
| git_last_commit_date: 2025-10-29 11:09:41 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-05 12:40 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4638 |
| 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 541/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.16.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz |
| StartedAt: 2025-11-04 22:48:20 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 23:00:55 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 755.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.16.0’
* 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
[2025-11-04 22:48:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:48:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-04 22:48:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-04
[2025-11-04 22:48:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-04 20:07:57 UTC; unix
[2025-11-04 22:48:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.0
[2025-11-04 22:48:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-04 22:48:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-04 22:48:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-04 22:48:53] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-04); AnnotationDbi 1.72.0(2025-11-04); AUCell 1.32.0(2025-11-04); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-04); Biobase 2.70.0(2025-11-04); BiocGenerics 0.56.0(2025-11-04); BiocParallel 1.44.0(2025-11-04); BiocSingular 1.26.0(2025-11-04); Biostrings 2.78.0(2025-11-04); 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 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-04); DelayedArray 0.36.0(2025-11-04); DelayedMatrixStats 1.32.0(2025-11-04); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-04); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-04); GSEABase 1.72.0(2025-11-04); GSVA 2.4.0(2025-11-04); h5mread 1.2.0(2025-11-04); HDF5Array 1.38.0(2025-11-04); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-04); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-04); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-04); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.18.0(2025-11-04); otel 0.2.0(2025-08-29); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-04); rhdf5filters 1.22.0(2025-11-04); Rhdf5lib 1.32.0(2025-11-04); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-04); S4Vectors 0.48.0(2025-11-04); ScaledMatrix 1.18.0(2025-11-04); Seqinfo 1.0.0(2025-11-04); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-04); SparseArray 1.10.1(2025-11-04); sparseMatrixStats 1.22.0(2025-11-04); SpatialExperiment 1.20.0(2025-11-04); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-04); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-04 22:48:53] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Contains 9 files.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:48:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-04 22:48:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-04 22:48:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-04 22:48:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-04 22:48:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:48:53] [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 29.152 1.834 39.037
get_dorothea 22.100 0.839 25.215
run_fgsea 22.360 0.405 22.775
run_aucell 9.097 1.673 10.795
get_progeny 6.199 0.282 12.919
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.16.0’ ** 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
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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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[2025-11-04 22:52:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:52:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-04 22:52:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-04
[2025-11-04 22:52:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-11-04 20:07:57 UTC; unix
[2025-11-04 22:52:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.0
[2025-11-04 22:52:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-04 22:52:18] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-08-23 r88802); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-04 22:52:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-04 22:52:19] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-04); AnnotationDbi 1.72.0(2025-11-04); AUCell 1.32.0(2025-11-04); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-04); Biobase 2.70.0(2025-11-04); BiocGenerics 0.56.0(2025-11-04); BiocParallel 1.44.0(2025-11-04); BiocSingular 1.26.0(2025-11-04); Biostrings 2.78.0(2025-11-04); 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 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-04); DelayedArray 0.36.0(2025-11-04); DelayedMatrixStats 1.32.0(2025-11-04); 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 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-04); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-04); ggplot2 4.0.0(2025-09-11); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-04); GSEABase 1.72.0(2025-11-04); GSVA 2.4.0(2025-11-04); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-04); HDF5Array 1.38.0(2025-11-04); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-04); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-04); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2025-11-04); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.0(2025-11-04); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); 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 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-04); rhdf5filters 1.22.0(2025-11-04); Rhdf5lib 1.32.0(2025-11-04); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.3(2025-08-20); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-04); S4Vectors 0.48.0(2025-11-04); S7 0.2.0(2024-11-07); ScaledMatrix 1.18.0(2025-11-04); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.0.0(2025-11-04); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-04); SparseArray 1.10.1(2025-11-04); sparseMatrixStats 1.22.0(2025-11-04); SpatialExperiment 1.20.0(2025-11-04); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-04); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-04); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-04); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-04 22:52:19] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Contains 9 files.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-04 22:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-04 22:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-04 22:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-04 22:52:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-11-04 22:52:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:52:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:52:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:21] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:21] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:21] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-04 22:52:21] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-04 22:52:21] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-04 22:52:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:52:21] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-04 22:52:21] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-04 22:52:22] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-11-04 22:52:22] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:52:22] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 1.01842s from www.ensembl.org (30.7 Kb/s); Redirect: 0.840858s, DNS look up: 0.004564s, Connection: 0.005919s, Pretransfer: 0.721702s, First byte at: 0.990401s
[2025-11-04 22:52:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Wed, 05 Nov 2025 03:52:21 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk; HTTP/2 302 ; date: Wed, 05 Nov 2025 03:52:21 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-94.us-east-2.compute.internal; HTTP/2 200 ; date: Wed, 05 Nov 2025 03:52:22 GMT; content-type: text/html; charset=utf-8; content-length: 31987; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Thu, 06 Nov 2025 03:47:58 GMT; set-cookie: ENSEMBL_WWW_SESSION=9da9e05c213122350db332a86959e2ee02f5b89a4603f1f6aedc3766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Thu, 06 Nov 2025 03:47:58 GMT; set-cookie: ENSEMBL_WWW_SESSION=9da9e05c213122350db332a86959e2ee02f5b89a4603f1f6aedc3766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-90.us-east-2.compute.internal
[2025-11-04 22:52:22] [TRACE] [OmnipathR] Response headers: [date=Wed, 05 Nov 2025 03:52:22 GMT,content-type=text/html; charset=utf-8,content-length=31987,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Thu, 06 Nov 2025 03:47:58 GMT,set-cookie=ENSEMBL_WWW_SESSION=9da9e05c213122350db332a86959e2ee02f5b89a4603f1f6aedc3766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Thu, 06 Nov 2025 03:47:58 GMT,set-cookie=ENSEMBL_WWW_SESSION=9da9e05c213122350db332a86959e2ee02f5b89a4603f1f6aedc3766; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-90.us-east-2.compute.internal]
[2025-11-04 22:52:23] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-11-04 22:52:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:23] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-11-04 22:52:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-04 22:52:24] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-04 22:52:24] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-04 22:52:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:52:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:52:24] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:52:24] [TRACE] [OmnipathR] Downloaded 4 Kb in 0.503219s from omabrowser.org (7.9 Kb/s); Redirect: 0s, DNS look up: 0.001861s, Connection: 0.002582s, Pretransfer: 0.411754s, First byte at: 0.503097s
[2025-11-04 22:52:24] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 05 Nov 2025 03:52:24 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-04 22:52:26] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:26] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-04 22:52:26] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:26] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-04 22:52:26] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-04 22:52:26] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-04 22:52:56] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-04 22:52:56] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-04 22:52:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:52:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:56] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-04 22:52:57] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-04 22:52:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:52:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-11-04 22:52:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:52:57] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:52:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:52:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:52:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:52:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:52:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.667158s from omnipathdb.org (23.5 Kb/s); Redirect: 0s, DNS look up: 0.001939s, Connection: 0.002744s, Pretransfer: 0.524858s, First byte at: 0.666171s
[2025-11-04 22:52:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:52:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:52:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:52:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-04 22:52:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:00] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:53:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-04 22:53:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-04 22:53:00] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-11-04 22:53:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:00] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-11-04 22:53:00] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-11-04 22:53:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:53:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:53:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:53:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:53:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:53:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:53:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.336655s from omnipathdb.org (46.5 Kb/s); Redirect: 0s, DNS look up: 0.002552s, Connection: 0.00326s, Pretransfer: 0.194669s, First byte at: 0.336292s
[2025-11-04 22:53:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:53:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:53:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:53:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:10] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:53:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-04 22:53:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-04 22:53:13] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-11-04 22:53:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:13] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-11-04 22:53:13] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2025-11-04 22:53:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:53:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:53:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-04 22:53:15] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:53:15] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:53:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-11-04 22:53:17] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-04 22:53:17] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2025-11-04 22:53:19] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-11-04 22:53:19] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:19] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-11-04 22:53:19] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-11-04 22:53:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:53:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:53:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:53:50] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:53:50] [TRACE] [OmnipathR] Downloaded 11 Kb in 30.844214s from omabrowser.org (365 bytes/s); Redirect: 0s, DNS look up: 0.001854s, Connection: 0.002583s, Pretransfer: 0.215985s, First byte at: 30.844109s
[2025-11-04 22:53:50] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 05 Nov 2025 03:53:50 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/tsv; charset=utf-8; content-length: 1187278; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2025-11-05_035349.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=8244793c6b91d491; expires=Fri, 05-Nov-2027 03:53:50 UTC; Path=/
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-11-04 22:53:53] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:53] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-11-04 22:53:53] [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`
[2025-11-04 22:53:53] [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`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:53:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:53:53] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-11-04 22:53:53] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-11-04 22:53:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:53:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:53:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:53:54] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:53:54] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.832577s from rest.uniprot.org (37 bytes/s); Redirect: 0s, DNS look up: 0.0044s, Connection: 0.005253s, Pretransfer: 0.476919s, First byte at: 0.832514s
[2025-11-04 22:53:54] [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: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 05 Nov 2025 03:53:54 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; 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: 15-October-2025
[2025-11-04 22:54:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-11-04 22:54:05] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-11-04 22:54:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:05] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-11-04 22:54:05] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] 13774 rows after translation; translated 13550 `uniprot_entry` IDs in column `id_organism_a` to 13550 `uniprot` IDs in column `id_organism_a`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-11-04 22:54:06] [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`
[2025-11-04 22:54:06] [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`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:06] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-11-04 22:54:06] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-04 22:54:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:54:06] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:54:06] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.50165s from rest.uniprot.org (61 bytes/s); Redirect: 0s, DNS look up: 0.005028s, Connection: 0.005952s, Pretransfer: 0.219279s, First byte at: 0.501608s
[2025-11-04 22:54:06] [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: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 05 Nov 2025 03:54:06 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; 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: 15-October-2025
[2025-11-04 22:54:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-11-04 22:54:12] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-11-04 22:54:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:12] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-11-04 22:54:12] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] 13774 rows after translation; translated 13253 `uniprot_entry` IDs in column `id_organism_b` to 13253 `uniprot` IDs in column `id_organism_b`.
[2025-11-04 22:54:13] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-04 22:54:13] [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`.
[2025-11-04 22:54:13] [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`
[2025-11-04 22:54:13] [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`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:13] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-11-04 22:54:13] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-11-04 22:54:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:54:13] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-04 22:54:13] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.508656s from rest.uniprot.org (84 bytes/s); Redirect: 0s, DNS look up: 0.016711s, Connection: 0.017621s, Pretransfer: 0.229325s, First byte at: 0.508607s
[2025-11-04 22:54:13] [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: 03-November-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 05 Nov 2025 03:54:13 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_04; 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: 15-October-2025
[2025-11-04 22:54:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-11-04 22:54:19] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:20] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-11-04 22:54:20] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] 163908 rows before translation, 12855 uniprot IDs in column `uniprot`.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] 163908 rows after translation; translated 12855 `uniprot` IDs in column `uniprot` to 12769 `genesymbol` IDs in column `genesymbol`.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [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`
[2025-11-04 22:54:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:54:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:54:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:54:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:54:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.379956s from omnipathdb.org (41.2 Kb/s); Redirect: 0s, DNS look up: 0.002217s, Connection: 0.002905s, Pretransfer: 0.228555s, First byte at: 0.379367s
[2025-11-04 22:54:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:54:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:54:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:54:25] [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`
[2025-11-04 22:54:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:25] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:54:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-11-04 22:54:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-11-04 22:54:26] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-11-04 22:54:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:26] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-11-04 22:54:35] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2025-11-04 22:54:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:54:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-11-04 22:54:45] [TRACE] [OmnipathR] Organism(s): 10090
[2025-11-04 22:54:45] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [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`
[2025-11-04 22:54:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:54:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:54:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:54:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:54:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.352944s from omnipathdb.org (44.4 Kb/s); Redirect: 0s, DNS look up: 0.001702s, Connection: 0.002283s, Pretransfer: 0.201985s, First byte at: 0.35206s
[2025-11-04 22:54:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:54:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:54:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:54:50] [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`
[2025-11-04 22:54:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:50] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:54:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-11-04 22:54:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-11-04 22:54:51] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-11-04 22:54:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:54:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:54:51] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-11-04 22:54:59] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:55:08] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:55:08] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:55:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:55:09] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.490623s from omnipathdb.org (31.9 Kb/s); Redirect: 0s, DNS look up: 0.002427s, Connection: 0.003064s, Pretransfer: 0.346674s, First byte at: 0.490043s
[2025-11-04 22:55:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:55:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:55:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:55:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:12] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:55:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-04 22:55:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-04 22:55:12] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-11-04 22:55:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:12] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-11-04 22:55:15] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2025-11-04 22:55:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:55:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-04 22:55:15] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:55:15] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:55:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:55:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-04 22:55:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-04 22:55:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-04 22:55:16] [TRACE] [OmnipathR] Downloaded 9 Kb in 0.467197s from omnipathdb.org (19.4 Kb/s); Redirect: 0s, DNS look up: 0.003306s, Connection: 0.004235s, Pretransfer: 0.391024s, First byte at: 0.466778s
[2025-11-04 22:55:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 05 Nov 2025 03:55:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 05 Nov 2025 04:55:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-04 22:55:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:17] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-04 22:55:17] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-04 22:55:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:17] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-04 22:55:17] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-04 22:55:18] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-11-04 22:55:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-11-04 22:55:20] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2025-11-04 22:55:20] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-04 22:55:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-11-04 22:55:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-04 22:55:20] [TRACE] [OmnipathR] Orthology targets:
[2025-11-04 22:55:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-04 22:55:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-04 22:55:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:21] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-11-04 22:55:21] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-11-04 22:55:21] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-11-04 22:55:21] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-11-04 22:55:21] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-11-04 22:55:22] [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 0 | WARN 18 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
179.120 15.973 271.741
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.073 | 0.014 | 0.087 | |
| convert_f_defaults | 0.058 | 0.022 | 0.080 | |
| decouple | 0.000 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.021 | 0.004 | 0.026 | |
| extract_sets | 0.021 | 0.001 | 0.022 | |
| filt_minsize | 0.040 | 0.003 | 0.043 | |
| get_collectri | 29.152 | 1.834 | 39.037 | |
| get_dorothea | 22.100 | 0.839 | 25.215 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 6.199 | 0.282 | 12.919 | |
| get_resource | 1.131 | 0.048 | 3.063 | |
| get_toy_data | 0.003 | 0.000 | 0.002 | |
| intersect_regulons | 0.028 | 0.001 | 0.030 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.036 | 0.007 | 0.044 | |
| run_aucell | 9.097 | 1.673 | 10.795 | |
| run_consensus | 1.876 | 0.217 | 2.093 | |
| run_fgsea | 22.360 | 0.405 | 22.775 | |
| run_gsva | 1.836 | 0.363 | 2.203 | |
| run_mdt | 0.137 | 0.027 | 0.161 | |
| run_mlm | 0.094 | 0.003 | 0.097 | |
| run_ora | 0.516 | 0.044 | 0.561 | |
| run_udt | 0.261 | 0.019 | 0.279 | |
| run_ulm | 0.072 | 0.007 | 0.080 | |
| run_viper | 0.987 | 0.169 | 1.159 | |
| run_wmean | 1.767 | 0.249 | 2.016 | |
| run_wsum | 0.710 | 0.076 | 0.783 | |
| show_methods | 0.049 | 0.013 | 0.061 | |
| show_resources | 0.181 | 0.044 | 0.866 | |
| tidyeval | 0 | 0 | 0 | |