Pau Badia-i-Mompel
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: devel |
| git_last_commit: 6010cb0 |
| git_last_commit_date: 2025-04-15 12:31:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 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" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 2.15.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 2.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.15.0.tar.gz |
| StartedAt: 2025-10-24 20:39:04 -0400 (Fri, 24 Oct 2025) |
| EndedAt: 2025-10-24 20:48:28 -0400 (Fri, 24 Oct 2025) |
| EllapsedTime: 564.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
[2025-10-24 20:39:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:39:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:40] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:39:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-24 20:39:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-24 20:39:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix
[2025-10-24 20:39:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-24 20:39:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-24 20:39:41] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-24 20:39:41] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-24 20:39:42] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-10-24); AnnotationDbi 1.71.2(2025-10-24); AUCell 1.31.0(2025-10-24); backports 1.5.0(2024-05-23); beachmat 2.25.5(2025-10-24); Biobase 2.69.1(2025-10-24); BiocGenerics 0.55.4(2025-10-24); BiocParallel 1.43.4(2025-10-24); BiocSingular 1.25.1(2025-10-24); Biostrings 2.77.2(2025-10-24); 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 2.15.0(2025-10-24); DelayedArray 0.35.3(2025-10-24); DelayedMatrixStats 1.31.0(2025-10-24); 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 1.61.6(2025-10-24); glue 1.8.0(2024-09-30); graph 1.87.0(2025-10-24); GSEABase 1.71.1(2025-10-24); GSVA 2.3.4(2025-10-24); h5mread 1.1.1(2025-10-24); HDF5Array 1.37.0(2025-10-24); 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 2.2.0(2025-10-13); IRanges 2.43.6(2025-10-24); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.2(2025-10-24); 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 1.21.0(2025-10-24); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.7(2025-10-24); 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 1.4.0(2025-10-22); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(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 2.53.6(2025-10-24); rhdf5filters 1.21.4(2025-10-24); Rhdf5lib 1.31.1(2025-10-24); 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 1.9.1(2025-10-24); S4Vectors 0.47.5(2025-10-24); ScaledMatrix 1.17.0(2025-10-24); Seqinfo 0.99.3(2025-10-24); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-10-24); SparseArray 1.9.1(2025-10-24); sparseMatrixStats 1.21.0(2025-10-24); SpatialExperiment 1.19.1(2025-10-24); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-10-24); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-10-24); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-24 20:39:42] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Contains 9 files.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-24 20:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-24 20:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-24 20:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-24 20:39:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:39:42] [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 34.562 4.310 48.015
get_dorothea 25.082 1.844 29.594
run_fgsea 24.708 1.351 26.270
run_aucell 12.464 4.292 16.814
get_progeny 6.784 0.636 14.194
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.15.0’ ** 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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
[2025-10-24 20:43:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:43:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-24 20:43:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-24
[2025-10-24 20:43:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-24 19:18:43 UTC; unix
[2025-10-24 20:43:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.7
[2025-10-24 20:43:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-24 20:43:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-24; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-10-24 20:43:52] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-24 20:43:52] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-10-24); AnnotationDbi 1.71.2(2025-10-24); AUCell 1.31.0(2025-10-24); backports 1.5.0(2024-05-23); beachmat 2.25.5(2025-10-24); Biobase 2.69.1(2025-10-24); BiocGenerics 0.55.4(2025-10-24); BiocParallel 1.43.4(2025-10-24); BiocSingular 1.25.1(2025-10-24); Biostrings 2.77.2(2025-10-24); 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); chromote 0.5.1(2025-04-24); 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 2.15.0(2025-10-24); DelayedArray 0.35.3(2025-10-24); DelayedMatrixStats 1.31.0(2025-10-24); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); 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 1.35.8(2025-10-24); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.6(2025-10-24); ggplot2 4.0.0(2025-09-11); glue 1.8.0(2024-09-30); graph 1.87.0(2025-10-24); GSEABase 1.71.1(2025-10-24); GSVA 2.3.4(2025-10-24); gtable 0.3.6(2024-10-25); h5mread 1.1.1(2025-10-24); HDF5Array 1.37.0(2025-10-24); 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 2.2.0(2025-10-13); IRanges 2.43.6(2025-10-24); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.2(2025-10-24); 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 1.21.0(2025-10-24); 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 3.17.7(2025-10-24); 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); plotly 4.11.0(2025-06-19); 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 1.4.0(2025-10-22); proxy 0.4-27(2022-06-09); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(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 2.53.6(2025-10-24); rhdf5filters 1.21.4(2025-10-24); Rhdf5lib 1.31.1(2025-10-24); 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 1.9.1(2025-10-24); S4Vectors 0.47.5(2025-10-24); S7 0.2.0(2024-11-07); ScaledMatrix 1.17.0(2025-10-24); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 0.99.3(2025-10-24); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-10-24); SparseArray 1.9.1(2025-10-24); sparseMatrixStats 1.21.0(2025-10-24); SpatialExperiment 1.19.1(2025-10-24); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-10-24); 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 1.43.0(2025-10-24); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-10-24); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-24 20:43:52] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Contains 9 files.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-24 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-24 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-24 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-24 20:43:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:52] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-10-24 20:43:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:43:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:54] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:54] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-24 20:43:54] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-24 20:43:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:43:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-24 20:43:54] [TRACE] [OmnipathR] Sending HTTP request.
[2025-10-24 20:43:55] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-10-24 20:43:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:43:55] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 1.033459s from www.ensembl.org (30.2 Kb/s); Redirect: 0.852222s, DNS look up: 0.00891s, Connection: 0.01055s, Pretransfer: 0.662023s, First byte at: 1.006093s
[2025-10-24 20:43:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 25 Oct 2025 00:43:55 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk; HTTP/2 302 ; date: Sat, 25 Oct 2025 00:43:55 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: Sat, 25 Oct 2025 00:43:55 GMT; content-type: text/html; charset=utf-8; content-length: 31940; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Sun, 26 Oct 2025 00:40:16 GMT; set-cookie: ENSEMBL_WWW_SESSION=f6d341132490501c0a489485694b36700569d54ca6315e0b090dac0f; 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=Sun, 26 Oct 2025 00:40:16 GMT; set-cookie: ENSEMBL_WWW_SESSION=f6d341132490501c0a489485694b36700569d54ca6315e0b090dac0f; 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
[2025-10-24 20:43:55] [TRACE] [OmnipathR] Response headers: [date=Sat, 25 Oct 2025 00:43:55 GMT,content-type=text/html; charset=utf-8,content-length=31940,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sun, 26 Oct 2025 00:40:16 GMT,set-cookie=ENSEMBL_WWW_SESSION=f6d341132490501c0a489485694b36700569d54ca6315e0b090dac0f; 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=Sun, 26 Oct 2025 00:40:16 GMT,set-cookie=ENSEMBL_WWW_SESSION=f6d341132490501c0a489485694b36700569d54ca6315e0b090dac0f; 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]
[2025-10-24 20:43:57] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:57] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-24 20:43:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:43:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:43:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-24 20:43:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-10-24 20:43:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:43:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:43:58] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:43:58] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.424708s from omabrowser.org (20.5 Kb/s); Redirect: 0s, DNS look up: 0.00146s, Connection: 0.002487s, Pretransfer: 0.339598s, First byte at: 0.424367s
[2025-10-24 20:43:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 25 Oct 2025 00:43:58 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
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-24 20:44:00] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:00] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-10-24 20:44:00] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:00] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-10-24 20:44:00] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-24 20:44:00] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-10-24 20:44:37] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:37] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-10-24 20:44:37] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:44:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:44:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:44:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:44:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.307032s from omnipathdb.org (51 Kb/s); Redirect: 0s, DNS look up: 0.001272s, Connection: 0.002289s, Pretransfer: 0.155702s, First byte at: 0.306566s
[2025-10-24 20:44:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:44:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:44:38 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:44:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:39] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-10-24 20:44:39] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:39] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-10-24 20:44:39] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-10-24 20:44:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:44:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:44:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-10-24 20:44:40] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:44:40] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:44:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:44:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:44:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:44:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.457125s from omnipathdb.org (34.3 Kb/s); Redirect: 0s, DNS look up: 0.001312s, Connection: 0.002205s, Pretransfer: 0.30633s, First byte at: 0.456689s
[2025-10-24 20:44:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:44:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:44:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:44:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:50] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:44:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-10-24 20:44:53] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-10-24 20:44:53] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-10-24 20:44:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:53] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-10-24 20:44:53] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2025-10-24 20:44:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:44:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-10-24 20:44:55] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:44:55] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:44:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:44:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:44:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:57] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-10-24 20:44:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-10-24 20:44:57] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2025-10-24 20:45:00] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-10-24 20:45:00] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-10-24 20:45:01] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:45:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:45:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:45:01] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-10-24 20:45:01] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-10-24 20:45:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:45:01] [TRACE] [OmnipathR] HTTP v2 GET: status 502.
[2025-10-24 20:45:01] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.418622s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001174s, Connection: 0.002138s, Pretransfer: 0.335196s, First byte at: 0.418532s
[2025-10-24 20:45:01] [TRACE] [OmnipathR] HTTP headers: HTTP/2 502 ; date: Sat, 25 Oct 2025 00:45:01 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/html; charset=UTF-8; content-length: 4636; etag: "652e5533-121c"
[2025-10-24 20:45:01] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000': The requested URL returned error: 502
[2025-10-24 20:45:01] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` (attempt 1/3); error: Failed to open 'https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000': The requested URL returned error: 502
[2025-10-24 20:45:06] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-10-24 20:45:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:45:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:45:41] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:45:41] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 34.715548s from omabrowser.org (326 bytes/s); Redirect: 0s, DNS look up: 0.001324s, Connection: 0.002311s, Pretransfer: 0.1892s, First byte at: 34.71536s
[2025-10-24 20:45:41] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 25 Oct 2025 00:45:41 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_2025-10-25_004539.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=1227dd34b549e26b; expires=Mon, 25-Oct-2027 00:45:41 UTC; Path=/
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-10-24 20:45:44] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:45:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:45:44] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-10-24 20:45:44] [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`
[2025-10-24 20:45:44] [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`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:45:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:45:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:45:44] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-10-24 20:45:44] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-10-24 20:45:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:45:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:45:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:45:51] [TRACE] [OmnipathR] Downloaded 31 bytes in 7.075164s from rest.uniprot.org (4 bytes/s); Redirect: 0s, DNS look up: 6.185567s, Connection: 6.186579s, Pretransfer: 6.71712s, First byte at: 7.07502s
[2025-10-24 20:45:51] [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: 15-October-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 25 Oct 2025 00:45:52 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
[2025-10-24 20:46:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-10-24 20:46:02] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-10-24 20:46:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:02] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-10-24 20:46:02] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-10-24 20:46:03] [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`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-10-24 20:46:03] [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`
[2025-10-24 20:46:03] [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`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:03] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-10-24 20:46:03] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-10-24 20:46:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:46:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:46:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:46:04] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.821907s from rest.uniprot.org (37 bytes/s); Redirect: 0s, DNS look up: 0.001275s, Connection: 0.002355s, Pretransfer: 0.487295s, First byte at: 0.821612s
[2025-10-24 20:46:04] [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: 15-October-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 25 Oct 2025 00:46:04 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
[2025-10-24 20:46:11] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-10-24 20:46:11] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-10-24 20:46:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:11] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-10-24 20:46:11] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-10-24 20:46:11] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-10-24 20:46:11] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-24 20:46:11] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-10-24 20:46:11] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-10-24 20:46:12] [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`.
[2025-10-24 20:46:12] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-10-24 20:46:12] [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`.
[2025-10-24 20:46:12] [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`
[2025-10-24 20:46:12] [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`.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:12] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-10-24 20:46:12] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-10-24 20:46:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:46:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-10-24 20:46:12] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.560298s from rest.uniprot.org (76 bytes/s); Redirect: 0s, DNS look up: 0.001218s, Connection: 0.002263s, Pretransfer: 0.272395s, First byte at: 0.560148s
[2025-10-24 20:46:12] [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: 15-October-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 25 Oct 2025 00:46:12 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
[2025-10-24 20:46:19] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-10-24 20:46:19] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-10-24 20:46:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:19] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-10-24 20:46:19] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] 163908 rows before translation, 12855 uniprot IDs in column `uniprot`.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] 163908 rows after translation; translated 12855 `uniprot` IDs in column `uniprot` to 12769 `genesymbol` IDs in column `genesymbol`.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [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`
[2025-10-24 20:46:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:46:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:46:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:46:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.463246s from omnipathdb.org (33.8 Kb/s); Redirect: 0s, DNS look up: 0.001174s, Connection: 0.002162s, Pretransfer: 0.31197s, First byte at: 0.462786s
[2025-10-24 20:46:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:46:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:46:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:46:25] [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`
[2025-10-24 20:46:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:25] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:46:25] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-10-24 20:46:27] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-10-24 20:46:27] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-10-24 20:46:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:27] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-10-24 20:46:38] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Organism(s): 10090
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [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`
[2025-10-24 20:46:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:46:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:46:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.444273s from omnipathdb.org (35.3 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.001928s, Pretransfer: 0.290673s, First byte at: 0.443792s
[2025-10-24 20:46:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:46:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:46:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:46:56] [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`
[2025-10-24 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:56] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:46:56] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-10-24 20:46:57] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-10-24 20:46:57] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-10-24 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:46:57] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-10-24 20:47:11] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:47:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:47:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.273357s from omnipathdb.org (57.3 Kb/s); Redirect: 0s, DNS look up: 0.001007s, Connection: 0.00183s, Pretransfer: 0.138699s, First byte at: 0.272851s
[2025-10-24 20:47:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:47:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:47:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:47:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:25] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:47:25] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-10-24 20:47:26] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-10-24 20:47:26] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-10-24 20:47:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:26] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-10-24 20:47:29] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2025-10-24 20:47:29] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:47:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-10-24 20:47:29] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:47:29] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:47:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:47:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [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`
[2025-10-24 20:47:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-10-24 20:47:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-10-24 20:47:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-10-24 20:47:30] [TRACE] [OmnipathR] Downloaded 9 Kb in 0.221599s from omnipathdb.org (40.8 Kb/s); Redirect: 0s, DNS look up: 0.001452s, Connection: 0.002677s, Pretransfer: 0.149218s, First byte at: 0.221201s
[2025-10-24 20:47:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 25 Oct 2025 00:47:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 25 Oct 2025 01:47:30 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-10-24 20:47:32] [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`
[2025-10-24 20:47:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:33] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-10-24 20:47:33] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-24 20:47:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:33] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-10-24 20:47:33] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-10-24 20:47:34] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2025-10-24 20:47:34] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:47:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-10-24 20:47:34] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:47:34] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:47:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:35] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-10-24 20:47:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-10-24 20:47:38] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2025-10-24 20:47:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-10-24 20:47:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Organism(s): 9606
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Orthology targets:
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-24 20:47:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-10-24 20:47:39] [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`
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-10-24 20:47:39] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-10-24 20:47:40] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
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
207.374 24.788 331.359
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.092 | 0.013 | 0.106 | |
| convert_f_defaults | 0.029 | 0.004 | 0.033 | |
| decouple | 0.001 | 0.001 | 0.002 | |
| dot-fit_preprocessing | 0.027 | 0.004 | 0.030 | |
| extract_sets | 0.027 | 0.002 | 0.029 | |
| filt_minsize | 0.046 | 0.001 | 0.047 | |
| get_collectri | 34.562 | 4.310 | 48.015 | |
| get_dorothea | 25.082 | 1.844 | 29.594 | |
| get_profile_of | 0.000 | 0.001 | 0.001 | |
| get_progeny | 6.784 | 0.636 | 14.194 | |
| get_resource | 0.909 | 0.091 | 2.372 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.033 | 0.008 | 0.043 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
| randomize_matrix | 0.001 | 0.001 | 0.000 | |
| rename_net | 0.048 | 0.010 | 0.059 | |
| run_aucell | 12.464 | 4.292 | 16.814 | |
| run_consensus | 2.660 | 0.629 | 3.308 | |
| run_fgsea | 24.708 | 1.351 | 26.270 | |
| run_gsva | 2.477 | 1.065 | 3.547 | |
| run_mdt | 0.183 | 0.053 | 0.245 | |
| run_mlm | 0.123 | 0.019 | 0.143 | |
| run_ora | 0.659 | 0.099 | 0.762 | |
| run_udt | 0.388 | 0.061 | 0.451 | |
| run_ulm | 0.104 | 0.020 | 0.125 | |
| run_viper | 1.180 | 0.530 | 1.739 | |
| run_wmean | 0.975 | 0.115 | 1.094 | |
| run_wsum | 1.018 | 0.122 | 1.147 | |
| show_methods | 0.062 | 0.014 | 0.077 | |
| show_resources | 0.066 | 0.007 | 0.625 | |
| tidyeval | 0 | 0 | 0 | |