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This page was generated on 2025-08-11 12:11 -0400 (Mon, 11 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4532
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 529/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.15.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2025-08-10 13:45 -0400 (Sun, 10 Aug 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)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for decoupleR on kjohnson3

To the developers/maintainers of the decoupleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: decoupleR
Version: 2.15.0
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: 2025-08-10 18:59:04 -0400 (Sun, 10 Aug 2025)
EndedAt: 2025-08-10 19:04:21 -0400 (Sun, 10 Aug 2025)
EllapsedTime: 316.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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 (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* 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
[2025-08-10 18:59:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 18:59:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:04:51 UTC; unix
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-10 18:59:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-10 18:59:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-10; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-08-10 18:59:19] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-10 18:59:19] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-10); AnnotationDbi 1.71.1(2025-08-10); AUCell 1.31.0(2025-08-10); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-10); Biobase 2.69.0(2025-08-10); BiocGenerics 0.55.1(2025-08-10); BiocParallel 1.43.4(2025-08-10); BiocSingular 1.25.0(2025-08-10); Biostrings 2.77.2(2025-08-10); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(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 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-08-10); DelayedArray 0.35.2(2025-08-10); DelayedMatrixStats 1.31.0(2025-08-10); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-08-10); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-10); GSEABase 1.71.0(2025-08-10); GSVA 2.3.1(2025-08-10); h5mread 1.1.1(2025-08-10); HDF5Array 1.37.0(2025-08-10); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-08-10); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-10); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.7(2025-06-06); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-10); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-10); parallelly 1.45.1(2025-07-24); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); 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 2.53.4(2025-08-10); rhdf5filters 1.21.0(2025-08-10); Rhdf5lib 1.31.0(2025-08-10); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-10); S4Vectors 0.47.0(2025-08-10); ScaledMatrix 1.17.0(2025-08-10); Seqinfo 0.99.2(2025-08-10); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-10); SparseArray 1.9.1(2025-08-10); sparseMatrixStats 1.21.0(2025-08-10); SpatialExperiment 1.19.1(2025-08-10); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-10); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-10); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-10 18:59:19] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Contains 9 files.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-10 18:59:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 18:59:19] [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  9.642  1.414  26.667
run_fgsea     10.362  0.461  12.244
get_dorothea   8.690  0.644  18.248
run_aucell     4.599  1.849  20.069
get_progeny    3.462  0.321  12.128
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [120] 0.112          | 0.112            [120]
  [121] 0.991          - 1.000            [121]
  [122] 0.991          - 1.000            [122]
  [123] 0.123          - 0.126            [123]
  [124] 0.123          - 0.126            [124]
  [125] 0.156          | 0.156            [125]
  [126] 0.156          | 0.156            [126]
  [127] 0.592          | 0.592            [127]
  
    `actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
  `expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
  
  [ FAIL 1 | WARN 18 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.


Installation output

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-arm64/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)

Tests output

decoupleR.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")

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[2025-08-10 19:01:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-10
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-10 19:04:51 UTC; unix
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-10 19:01:35] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-10; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-08-10 19:01:36] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-10 19:01:36] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-10); AnnotationDbi 1.71.1(2025-08-10); AUCell 1.31.0(2025-08-10); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-10); Biobase 2.69.0(2025-08-10); BiocGenerics 0.55.1(2025-08-10); BiocParallel 1.43.4(2025-08-10); BiocSingular 1.25.0(2025-08-10); Biostrings 2.77.2(2025-08-10); 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 1.0.9(2025-07-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); 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 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-08-10); DelayedArray 0.35.2(2025-08-10); DelayedMatrixStats 1.31.0(2025-08-10); 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 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.35.6(2025-08-10); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-08-10); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-10); GSEABase 1.71.0(2025-08-10); GSVA 2.3.1(2025-08-10); gtable 0.3.6(2024-10-25); h5mread 1.1.1(2025-08-10); HDF5Array 1.37.0(2025-08-10); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-08-10); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-10); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.7(2025-06-06); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-10); 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 3.17.4(2025-08-10); parallelly 1.45.1(2025-07-24); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); 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 2.53.4(2025-08-10); rhdf5filters 1.21.0(2025-08-10); Rhdf5lib 1.31.0(2025-08-10); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); rpart 4.1.24(2025-01-07); RSQLite 2.4.2(2025-07-18); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-10); S4Vectors 0.47.0(2025-08-10); ScaledMatrix 1.17.0(2025-08-10); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 0.99.2(2025-08-10); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-10); SparseArray 1.9.1(2025-08-10); sparseMatrixStats 1.21.0(2025-08-10); SpatialExperiment 1.19.1(2025-08-10); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-10); 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(2025-08-10); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-10); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-10 19:01:36] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Contains 9 files.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:36] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-08-10 19:01:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-08-10 19:01:37] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-08-10 19:01:38] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-08-10 19:01:38] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:01:38] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.986884s from www.ensembl.org (31.5 Kb/s); Redirect: 0.80064s, DNS look up: 0.005575s, Connection: 0.007358s, Pretransfer: 0.681577s, First byte at: 0.958589s
[2025-08-10 19:01:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sun, 10 Aug 2025 23:01:38 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-p1m2-31.ebi.ac.uk; HTTP/2 302 ; date: Sun, 10 Aug 2025 23:01:38 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-10-25-25-73.us-east-2.compute.internal; HTTP/2 200 ; date: Sun, 10 Aug 2025 23:01:38 GMT; content-type: text/html; charset=utf-8; content-length: 31866; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Mon, 11 Aug 2025 23:00:00 GMT; set-cookie: ENSEMBL_WWW_SESSION=933bb49d1d528e210bba885a68e83e7006a5ddb2f5cfb688f855aa0a; 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=Mon, 11 Aug 2025 23:00:00 GMT; set-cookie: ENSEMBL_WWW_SESSION=933bb49d1d528e210bba885a68e83e7006a5ddb2f5cfb688f855aa0a; 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-10-25-25-92.us-east-2.compute.internal
[2025-08-10 19:01:38] [TRACE]   [OmnipathR] Response headers: [date=Sun, 10 Aug 2025 23:01:38 GMT,content-type=text/html; charset=utf-8,content-length=31866,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Mon, 11 Aug 2025 23:00:00 GMT,set-cookie=ENSEMBL_WWW_SESSION=933bb49d1d528e210bba885a68e83e7006a5ddb2f5cfb688f855aa0a; 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=Mon, 11 Aug 2025 23:00:00 GMT,set-cookie=ENSEMBL_WWW_SESSION=933bb49d1d528e210bba885a68e83e7006a5ddb2f5cfb688f855aa0a; 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-10-25-25-92.us-east-2.compute.internal]
[2025-08-10 19:01:39] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:39] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-10 19:01:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:39] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-10 19:01:39] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:01:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-10 19:01:40] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:01:40] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.435702s from omabrowser.org (19.9 Kb/s); Redirect: 0s, DNS look up: 0.0041s, Connection: 0.013974s, Pretransfer: 0.349075s, First byte at: 0.435508s
[2025-08-10 19:01:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sun, 10 Aug 2025 23:01:40 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
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-10 19:01:41] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:41] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-08-10 19:01:41] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:41] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-08-10 19:01:41] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-10 19:01:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-08-10 19:01:55] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:55] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-08-10 19:01:55] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:01:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:01:56] [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]
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.303702s from omnipathdb.org (51.6 Kb/s); Redirect: 0s, DNS look up: 0.009299s, Connection: 0.010291s, Pretransfer: 0.155975s, First byte at: 0.303471s
[2025-08-10 19:01:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:01:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:01:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:01:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:57] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-08-10 19:01:57] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:57] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-08-10 19:01:57] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:01:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:01:58] [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]
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.462307s from omnipathdb.org (33.9 Kb/s); Redirect: 0s, DNS look up: 0.001321s, Connection: 0.002835s, Pretransfer: 0.309989s, First byte at: 0.462077s
[2025-08-10 19:01:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:01:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:01:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:02:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:02:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:06] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:02:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-10 19:02:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-10 19:02:07] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-08-10 19:02:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:07] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-08-10 19:02:07] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:02:08] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:02:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:02:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:02:10] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-10 19:02:10] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-10 19:02:10] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-08-10 19:02:11] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-08-10 19:02:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:11] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-08-10 19:02:11] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-10 19:02:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:02:11] [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]
[2025-08-10 19:02:42] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:02:42] [TRACE]   [OmnipathR] Downloaded 11.3 Kb in 31.042118s from omabrowser.org (374 bytes/s); Redirect: 0s, DNS look up: 0.001306s, Connection: 0.002261s, Pretransfer: 0.167072s, First byte at: 31.041839s
[2025-08-10 19:02:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sun, 10 Aug 2025 23:02:42 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_2025-08-10_230240.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=1a5495fd28391a38; expires=Tue, 10-Aug-2027 23:02:42 UTC; Path=/
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-08-10 19:02:44] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:44] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-08-10 19:02:44] [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`
[2025-08-10 19:02:44] [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`.
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:02:44] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-08-10 19:02:44] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-08-10 19:02:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:02:45] [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]
[2025-08-10 19:02:45] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:02:45] [TRACE]   [OmnipathR] Downloaded 31 bytes in 0.85679s from rest.uniprot.org (36 bytes/s); Redirect: 0s, DNS look up: 0.011052s, Connection: 0.01294s, Pretransfer: 0.510696s, First byte at: 0.855064s
[2025-08-10 19:02:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sun, 10 Aug 2025 23:02:45 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; access-control-allow-origin: *; 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: 18-June-2025
[2025-08-10 19:03:01] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-08-10 19:03:01] [INFO]    [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-08-10 19:03:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:01] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:01] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-08-10 19:03:02] [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`.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-08-10 19:03:02] [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`
[2025-08-10 19:03:02] [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`.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:02] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-08-10 19:03:02] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-10 19:03:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:02] [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]
[2025-08-10 19:03:03] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:03:03] [TRACE]   [OmnipathR] Downloaded 31 bytes in 0.604435s from rest.uniprot.org (51 bytes/s); Redirect: 0s, DNS look up: 0.001176s, Connection: 0.002086s, Pretransfer: 0.243015s, First byte at: 0.601188s
[2025-08-10 19:03:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sun, 10 Aug 2025 23:03:03 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; access-control-allow-origin: *; 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: 18-June-2025
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-08-10 19:03:10] [INFO]    [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:10] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:10] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-08-10 19:03:10] [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`.
[2025-08-10 19:03:10] [INFO]    [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-08-10 19:03:10] [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`.
[2025-08-10 19:03:10] [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`
[2025-08-10 19:03:10] [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`.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:10] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-08-10 19:03:10] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-10 19:03:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:10] [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]
[2025-08-10 19:03:11] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-08-10 19:03:11] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.585218s from rest.uniprot.org (73 bytes/s); Redirect: 0s, DNS look up: 0.009651s, Connection: 0.010782s, Pretransfer: 0.254729s, First byte at: 0.584808s
[2025-08-10 19:03:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; 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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sun, 10 Aug 2025 23:03:11 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; access-control-allow-origin: *; 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: 18-June-2025
[2025-08-10 19:03:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-08-10 19:03:17] [INFO]    [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-08-10 19:03:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:17] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:17] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] 163950 rows before translation, 12858 uniprot IDs in column `uniprot`.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] 163950 rows after translation; translated 12858 `uniprot` IDs in column `uniprot` to 12772 `genesymbol` IDs in column `genesymbol`.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [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`
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:18] [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]
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.305808s from omnipathdb.org (51.2 Kb/s); Redirect: 0s, DNS look up: 0.000916s, Connection: 0.001782s, Pretransfer: 0.155085s, First byte at: 0.305621s
[2025-08-10 19:03:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:03:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:03:18 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:03:22] [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`
[2025-08-10 19:03:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:22] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-08-10 19:03:23] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-08-10 19:03:23] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-08-10 19:03:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:23] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:30] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Organism(s): 10090
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [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`
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.31334s from omnipathdb.org (50 Kb/s); Redirect: 0s, DNS look up: 0.001136s, Connection: 0.002022s, Pretransfer: 0.158898s, First byte at: 0.312954s
[2025-08-10 19:03:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:03:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:03:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:03:39] [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`
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:39] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-08-10 19:03:39] [INFO]    [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:39] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:47] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:51] [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]
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.323737s from omnipathdb.org (48.4 Kb/s); Redirect: 0s, DNS look up: 0.001344s, Connection: 0.002447s, Pretransfer: 0.167537s, First byte at: 0.319985s
[2025-08-10 19:03:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:03:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:03:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:03:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:54] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-10 19:03:54] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:54] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:55] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [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`
[2025-08-10 19:03:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-10 19:03:55] [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]
[2025-08-10 19:03:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-08-10 19:03:56] [TRACE]   [OmnipathR] Downloaded 9.5 Kb in 0.239945s from omnipathdb.org (39.6 Kb/s); Redirect: 0s, DNS look up: 0.000958s, Connection: 0.001897s, Pretransfer: 0.157738s, First byte at: 0.23897s
[2025-08-10 19:03:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sun, 10 Aug 2025 23:03:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 11 Aug 2025 00:03:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-10 19:03:57] [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`
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:57] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-10 19:03:57] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:57] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-08-10 19:03:57] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:03:57] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:57] [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`
[2025-08-10 19:03:58] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-10 19:03:58] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-10 19:03:58] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Orthology targets: 
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-10 19:03:59] [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`
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-10 19:03:59] [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`
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-08-10 19:03:59] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-08-10 19:03:59] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache.

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Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

[ FAIL 1 | WARN 18 | SKIP 0 | PASS 34 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).

actual vs expected
                      p_value
  actual[1, ]     0.075479709
  actual[2, ]     0.075479709
- actual[3, ]     0.511687342
+ expected[3, ]   0.548454870
- actual[4, ]     0.511687342
+ expected[4, ]   0.548454870
  actual[5, ]     0.010000000
  actual[6, ]     0.010000000
  actual[7, ]     0.076411558

actual vs expected
                      p_value
  actual[12, ]    0.010000000
  actual[13, ]    0.114238030
  actual[14, ]    0.114238030
- actual[15, ]    0.510665738
+ expected[15, ]  0.522337972
- actual[16, ]    0.510665738
+ expected[16, ]  0.522337972
  actual[17, ]    0.010000000
  actual[18, ]    0.010000000
  actual[19, ]    0.004682543
  actual[20, ]    0.004682543
- actual[21, ]    0.219233595
+ expected[21, ]  0.294730294
and 10 more ...

actual vs expected
                      p_value
  actual[34, ]    1.000000000
  actual[35, ]    0.010000000
  actual[36, ]    0.010000000
- actual[37, ]    0.091542106
+ expected[37, ]  0.103646587
- actual[38, ]    0.091542106
+ expected[38, ]  0.103646587
  actual[39, ]    0.592371428
  actual[40, ]    0.592371428
  actual[41, ]    0.010000000

actual vs expected
                      p_value
  actual[52, ]    0.976649086
  actual[53, ]    0.010000000
  actual[54, ]    0.010000000
- actual[55, ]    0.066624941
+ expected[55, ]  0.076411558
- actual[56, ]    0.066624941
+ expected[56, ]  0.076411558
  actual[57, ]    0.592371428
  actual[58, ]    0.592371428
  actual[59, ]    0.010000000
  actual[60, ]    0.010000000
- actual[61, ]    0.111211902
+ expected[61, ]  0.108185775
and 4 more ...

actual vs expected
                      p_value
  actual[70, ]    1.000000000
  actual[71, ]    0.010000000
  actual[72, ]    0.010000000
- actual[73, ]    0.256981914
+ expected[73, ]  0.469812943
- actual[74, ]    0.256981914
+ expected[74, ]  0.469812943
- actual[75, ]    0.133907888
+ expected[75, ]  0.132394821
- actual[76, ]    0.133907888
+ expected[76, ]  0.132394821
  actual[77, ]    0.123204721
  actual[78, ]    0.123204721
- actual[79, ]    0.146641013
+ expected[79, ]  0.207618744
and 4 more ...

actual vs expected
                      p_value
  actual[88, ]    0.177906190
  actual[89, ]    0.154281338
  actual[90, ]    0.154281338
- actual[91, ]    0.434796297
+ expected[91, ]  0.487321278
- actual[92, ]    0.434796297
+ expected[92, ]  0.487321278
  actual[93, ]    0.009411332
  actual[94, ]    0.009411332
  actual[95, ]    0.005020222
  actual[96, ]    0.005020222
- actual[97, ]    0.294730294
+ expected[97, ]  0.493157392
and 16 more ...

actual vs expected
                      p_value
  actual[118, ]   0.126342554
  actual[119, ]   0.111593916
  actual[120, ]   0.111593916
- actual[121, ]   0.991185346
+ expected[121, ] 1.000000000
- actual[122, ]   0.991185346
+ expected[122, ] 1.000000000
- actual[123, ]   0.123316421
+ expected[123, ] 0.126342554
- actual[124, ]   0.123316421
+ expected[124, ] 0.126342554
  actual[125, ]   0.155922629
  actual[126, ]   0.155922629
  actual[127, ]   0.592371428

actual vs expected
                      p_value
  actual[132, ]   0.124515409
  actual[133, ]   0.592371428
  actual[134, ]   0.592371428
- actual[135, ]   0.174865133
+ expected[135, ] 0.183988307
- actual[136, ]   0.174865133
+ expected[136, ] 0.183988307
  actual[137, ]   0.198360798
  actual[138, ]   0.198360798
  actual[139, ]   0.592371428

  `actual$p_value[1:7]`: 0.075 0.075 0.512 0.512 0.010 0.010 0.076
`expected$p_value[1:7]`: 0.075 0.075 0.548 0.548 0.010 0.010 0.076

     actual$p_value | expected$p_value                
[12] 0.010          | 0.010            [12]           
[13] 0.114          | 0.114            [13]           
[14] 0.114          | 0.114            [14]           
[15] 0.511          - 0.522            [15]           
[16] 0.511          - 0.522            [16]           
[17] 0.010          | 0.010            [17]           
[18] 0.010          | 0.010            [18]           
[19] 0.005          | 0.005            [19]           
[20] 0.005          | 0.005            [20]           
[21] 0.219          - 0.295            [21]           
 ... ...              ...              and 10 more ...

  `actual$p_value[34:41]`: 1.000 0.010 0.010 0.092 0.092 0.592 0.592 0.010
`expected$p_value[34:41]`: 1.000 0.010 0.010 0.104 0.104 0.592 0.592 0.010

     actual$p_value | expected$p_value               
[52] 0.977          | 0.977            [52]          
[53] 0.010          | 0.010            [53]          
[54] 0.010          | 0.010            [54]          
[55] 0.067          - 0.076            [55]          
[56] 0.067          - 0.076            [56]          
[57] 0.592          | 0.592            [57]          
[58] 0.592          | 0.592            [58]          
[59] 0.010          | 0.010            [59]          
[60] 0.010          | 0.010            [60]          
[61] 0.111          - 0.108            [61]          
 ... ...              ...              and 4 more ...

     actual$p_value | expected$p_value               
[70] 1.000          | 1.000            [70]          
[71] 0.010          | 0.010            [71]          
[72] 0.010          | 0.010            [72]          
[73] 0.257          - 0.470            [73]          
[74] 0.257          - 0.470            [74]          
[75] 0.134          - 0.132            [75]          
[76] 0.134          - 0.132            [76]          
[77] 0.123          | 0.123            [77]          
[78] 0.123          | 0.123            [78]          
[79] 0.147          - 0.208            [79]          
 ... ...              ...              and 4 more ...

     actual$p_value | expected$p_value                
[88] 0.178          | 0.178            [88]           
[89] 0.154          | 0.154            [89]           
[90] 0.154          | 0.154            [90]           
[91] 0.435          - 0.487            [91]           
[92] 0.435          - 0.487            [92]           
[93] 0.009          | 0.009            [93]           
[94] 0.009          | 0.009            [94]           
[95] 0.005          | 0.005            [95]           
[96] 0.005          | 0.005            [96]           
[97] 0.295          - 0.493            [97]           
 ... ...              ...              and 16 more ...

      actual$p_value | expected$p_value      
[118] 0.126          | 0.126            [118]
[119] 0.112          | 0.112            [119]
[120] 0.112          | 0.112            [120]
[121] 0.991          - 1.000            [121]
[122] 0.991          - 1.000            [122]
[123] 0.123          - 0.126            [123]
[124] 0.123          - 0.126            [124]
[125] 0.156          | 0.156            [125]
[126] 0.156          | 0.156            [126]
[127] 0.592          | 0.592            [127]

  `actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592

[ FAIL 1 | WARN 18 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.0290.0030.033
convert_f_defaults0.0080.0010.010
decouple000
dot-fit_preprocessing0.0080.0010.009
extract_sets0.0070.0010.012
filt_minsize0.0110.0000.012
get_collectri 9.642 1.41426.667
get_dorothea 8.690 0.64418.248
get_profile_of000
get_progeny 3.462 0.32112.128
get_resource0.3380.0482.452
get_toy_data0.0010.0000.002
intersect_regulons0.0130.0060.096
pipe000
pivot_wider_profile000
randomize_matrix0.0000.0000.001
rename_net0.0170.0070.107
run_aucell 4.599 1.84920.069
run_consensus0.8620.2212.371
run_fgsea10.362 0.46112.244
run_gsva0.7480.4532.397
run_mdt0.0520.0190.088
run_mlm0.0290.0050.049
run_ora0.1570.0350.300
run_udt0.0930.0230.175
run_ulm0.0270.0070.089
run_viper0.3290.1831.024
run_wmean0.2270.0390.461
run_wsum0.2360.0510.426
show_methods0.0180.0050.036
show_resources0.0210.0040.566
tidyeval000