Multiple platform build/check report for BioC 3.23 - CHECK results for decoupleR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4988
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4694
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*

CHECK results for decoupleR on nebbiolo1

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: 2.18.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings decoupleR_2.18.0.tar.gz

StartedAt: 2026-04-28 23:29:59 -0400 (Tue, 28 Apr 2026)

EndedAt: 2026-04-28 23:54:32 -0400 (Tue, 28 Apr 2026)

EllapsedTime: 1473.9 seconds

RetCode: 1

Status: ERROR

CheckDir: decoupleR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings decoupleR_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/decoupleR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-29 03:29:59 UTC
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2026-04-28 23:30:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:30:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-28
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-28 19:28:53 UTC; unix
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-04-28 23:30:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-28 23:30:36] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-28 23:30:36] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-28 23:30:36] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.90.0(2026-04-28); AnnotationDbi 1.74.0(2026-04-28); AUCell 1.34.0(2026-04-28); backports 1.5.1(2026-04-03); beachmat 2.28.0(2026-04-28); Biobase 2.72.0(2026-04-28); BiocGenerics 0.58.0(2026-04-28); BiocParallel 1.46.0(2026-04-28); BiocSingular 1.28.0(2026-04-28); Biostrings 2.80.0(2026-04-28); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.18.0(2026-04-28); DelayedArray 0.38.0(2026-04-28); DelayedMatrixStats 1.34.0(2026-04-28); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicRanges 1.64.0(2026-04-28); glue 1.8.1(2026-04-17); graph 1.90.0(2026-04-28); GSEABase 1.74.0(2026-04-28); GSVA 2.6.0(2026-04-28); h5mread 1.4.0(2026-04-28); HDF5Array 1.40.0(2026-04-28); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); IRanges 2.46.0(2026-04-28); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.52.0(2026-04-28); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.5(2026-04-04); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.24.0(2026-04-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); OmnipathR 4.0.0(2026-04-28); otel 0.2.0(2025-08-29); parallelly 1.47.0(2026-04-17); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); processx 3.9.0(2026-04-22); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.3(2026-04-20); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.56.0(2026-04-28); rhdf5filters 1.24.0(2026-04-28); Rhdf5lib 2.0.0(2026-04-28); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.12.0(2026-04-28); S4Vectors 0.50.0(2026-04-28); ScaledMatrix 1.20.0(2026-04-28); Seqinfo 1.2.0(2026-04-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.34.0(2026-04-28); SparseArray 1.12.0(2026-04-28); sparseMatrixStats 1.24.0(2026-04-28); SpatialExperiment 1.22.0(2026-04-28); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.42.0(2026-04-28); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.52.0(2026-04-28); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-28 23:30:36] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Contains 1 files.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-28 23:30:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:30:36] [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 32.542  2.464  41.196
get_dorothea  23.423  1.121  26.230
run_fgsea     23.304  0.461  23.750
run_aucell     8.420  1.809  10.166
get_progeny    6.719  0.412  12.530
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   [3] 0.519          - 0.548            [3]             
   [4] 0.519          - 0.548            [4]             
   [5] 0.010          | 0.010            [5]             
   [6] 0.010          | 0.010            [6]             
   [7] 0.087          - 0.076            [7]             
   [8] 0.087          - 0.076            [8]             
   [9] 1.000          - 0.977            [9]             
  [10] 1.000          - 0.977            [10]            
   ... ...              ...              and 134 more ...
  
  
  [ FAIL 3 | WARN 9 | SKIP 0 | PASS 32 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/decoupleR.Rcheck/00check.log’
for details.

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘decoupleR’ ...
** this is package ‘decoupleR’ version ‘2.18.0’
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(decoupleR)
> 
> test_check("decoupleR")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

Warning: stack imbalance in '.Call', 162 then 164
Saving _problems/test-decoupleR-decouple-82.R
[2026-04-28 23:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-28
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-28 19:28:53 UTC; unix
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-28 23:34:11] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-28 23:34:12] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-28 23:34:12] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.90.0(2026-04-28); AnnotationDbi 1.74.0(2026-04-28); AUCell 1.34.0(2026-04-28); backports 1.5.1(2026-04-03); beachmat 2.28.0(2026-04-28); Biobase 2.72.0(2026-04-28); BiocGenerics 0.58.0(2026-04-28); BiocParallel 1.46.0(2026-04-28); BiocSingular 1.28.0(2026-04-28); Biostrings 2.80.0(2026-04-28); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); broom 1.0.12(2026-01-27); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); class 7.3-23(2025-01-01); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.18.0(2026-04-28); DelayedArray 0.38.0(2026-04-28); DelayedMatrixStats 1.34.0(2026-04-28); desc 1.4.3(2023-12-10); diffobj 0.3.6(2025-04-21); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); e1071 1.7-17(2025-12-18); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.38.0(2026-04-28); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicRanges 1.64.0(2026-04-28); ggplot2 4.0.3(2026-04-22); glue 1.8.1(2026-04-17); graph 1.90.0(2026-04-28); GSEABase 1.74.0(2026-04-28); GSVA 2.6.0(2026-04-28); gtable 0.3.6(2024-10-25); h5mread 1.4.0(2026-04-28); HDF5Array 1.40.0(2026-04-28); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); IRanges 2.46.0(2026-04-28); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.52.0(2026-04-28); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lazyeval 0.2.3(2026-04-04); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.5(2026-04-04); MASS 7.3-65(2025-02-28); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.24.0(2026-04-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); mixtools 2.0.0.1(2025-03-08); nlme 3.1-169(2026-03-27); OmnipathR 4.0.0(2026-04-28); otel 0.2.0(2025-08-29); parallelly 1.47.0(2026-04-17); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-29(2025-12-29); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.18.0(2026-01-16); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.56.0(2026-04-28); rhdf5filters 1.24.0(2026-04-28); Rhdf5lib 2.0.0(2026-04-28); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); rpart 4.1.27(2026-03-27); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.12.0(2026-04-28); S4Vectors 0.50.0(2026-04-28); S7 0.2.2(2026-04-22); ScaledMatrix 1.20.0(2026-04-28); scales 1.4.0(2025-04-24); segmented 2.2-1(2026-01-29); Seqinfo 1.2.0(2026-04-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.34.0(2026-04-28); SparseArray 1.12.0(2026-04-28); sparseMatrixStats 1.24.0(2026-04-28); SpatialExperiment 1.22.0(2026-04-28); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.42.0(2026-04-28); survival 3.8-6(2026-01-16); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); viper 1.46.0(2026-04-28); viridisLite 0.4.3(2026-02-04); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.52.0(2026-04-28); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-28 23:34:12] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Contains 10 files.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-04-28 23:34:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:34:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:14] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-04-28 23:34:14] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:14] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:14] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-04-28 23:34:14] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-04-28 23:34:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-04-28 23:34:15] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-04-28 23:34:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:34:15] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.583239s from rescued.omnipathdb.org (68.3 Kb/s); Redirect: 0s, DNS look up: 0.001491s, Connection: 0.002264s, Pretransfer: 0.300709s, First byte at: 0.443756s
[2026-04-28 23:34:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:34:14 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Wed, 29 Apr 2026 04:34:14 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-04-28 23:34:15] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Wed, 29 Apr 2026 03:34:14 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Wed, 29 Apr 2026 04:34:14 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-04-28 23:34:16] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:16] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-28 23:34:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:16] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-28 23:34:16] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-04-28 23:34:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:34:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:34:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:34:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:34:17] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.485006s from omabrowser.org (15.6 Kb/s); Redirect: 0s, DNS look up: 0.000918s, Connection: 0.014225s, Pretransfer: 0.055936s, First byte at: 0.484766s
[2026-04-28 23:34:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 29 Apr 2026 03:34:17 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=nY%2BFAy5HGF4XecMREogATPCLtIaGzSjbzNkvgbv3fHDY5w99gA%2BXf4G%2FEkbBUCBE79byijeQHjmk3ipNkAjcxcWgJ4v7%2BlLInMFLLJWiu3Vn2m0h9Ulq1rKAkcys0a15tg%3D%3D"}]}; cf-ray: 9f3b4004be24d6db-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-28 23:34:18] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-28 23:34:18] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-04-28 23:34:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:19] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-28 23:34:19] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:19] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-28 23:34:19] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-28 23:34:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-04-28 23:34:50] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:50] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:50] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:34:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-04-28 23:34:51] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:51] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-04-28 23:34:51] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=TFcensus,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:34:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=TFcensus,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:34:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:34:53] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:34:53] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.31263s from omnipathdb.org (50.2 Kb/s); Redirect: 0s, DNS look up: 0.00155s, Connection: 0.002259s, Pretransfer: 0.157196s, First byte at: 0.312142s
[2026-04-28 23:34:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:34:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:34:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:34:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:54] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-04-28 23:34:54] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:54] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2026-04-28 23:34:54] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-04-28 23:34:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=PROGENy,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:34:55] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=PROGENy,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.310156s from omnipathdb.org (50.6 Kb/s); Redirect: 0s, DNS look up: 0.001434s, Connection: 0.002097s, Pretransfer: 0.156219s, First byte at: 0.309722s
[2026-04-28 23:34:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:34:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:34:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:35:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:35:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:04] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:35:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-28 23:35:07] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-28 23:35:07] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-04-28 23:35:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:07] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-04-28 23:35:07] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2026-04-28 23:35:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=PROGENy,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:35:09] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:35:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:10] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=PROGENy,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:35:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:35:12] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-04-28 23:35:12] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-04-28 23:35:12] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2026-04-28 23:35:14] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Checking on-disk cache for database `oma`.
[2026-04-28 23:35:14] [INFO]    [OmnipathR] Cache record does not exist: `db://oma`
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Loading database `oma` from source.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-28 23:35:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:14] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-28 23:35:14] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:35:14] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:35:32] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:35:32] [TRACE]   [OmnipathR] Downloaded 12.7 Kb in 17.157546s from omabrowser.org (757 bytes/s); Redirect: 0s, DNS look up: 0.000873s, Connection: 0.014233s, Pretransfer: 0.090285s, First byte at: 17.157359s
[2026-04-28 23:35:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 29 Apr 2026 03:35:32 GMT; content-type: text/tsv; charset=utf-8; content-length: 1187278; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2026-04-29_033531.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=73d0113761fa7ad3; expires=Fri, 28-Apr-2028 03:35:32 UTC; Path=/; cf-cache-status: DYNAMIC; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=TF6WSV72ut1Pje6fu667ausHL0Z5Z5xjnsfD3yxVoAr6kxqmW5nx1YN%2BqMy%2FJ0LjnB0rJHWksQtWXRFDzZVhTRFkWqnouDKyQKwQgJ4jzYZOjoLNLfcO6pPrb7p%2FEFaQJg%3D%3D"}]}; cf-ray: 9f3b416eef8b07b5-IAD; alt-svc: h3=":443"; ma=86400
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-04-28 23:35:34] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:34] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-28 23:35:34] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:35:34] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-28 23:35:34] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:35:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:35:36] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:35:36] [TRACE]   [OmnipathR] Downloaded 31 bytes in 1.584373s from rest.uniprot.org (19 bytes/s); Redirect: 0s, DNS look up: 0.00334s, Connection: 0.00414s, Pretransfer: 0.656705s, First byte at: 1.584319s
[2026-04-28 23:35:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:35:36 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-04-28 23:38:27] [INFO]    [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:38:27] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2026-04-28 23:38:27] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] 13774 rows after translation; translated 13523 `uniprot_entry` IDs in column `id_organism_a` to 13523 `uniprot` IDs in column `id_organism_a`.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-04-28 23:38:27] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-28 23:38:28] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:38:28] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-28 23:38:28] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:38:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:38:29] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:38:29] [TRACE]   [OmnipathR] Downloaded 31 bytes in 1.871349s from rest.uniprot.org (16 bytes/s); Redirect: 0s, DNS look up: 0.002542s, Connection: 0.003269s, Pretransfer: 0.487163s, First byte at: 1.871306s
[2026-04-28 23:38:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:38:29 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:40:41] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-28 23:40:46] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:40:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:40:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:40:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:40:48] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:40:48] [TRACE]   [OmnipathR] Downloaded 31 bytes in 1.817909s from rest.uniprot.org (17 bytes/s); Redirect: 0s, DNS look up: 0.001463s, Connection: 0.002127s, Pretransfer: 0.497257s, First byte at: 1.817855s
[2026-04-28 23:40:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:40:48 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-04-28 23:42:36] [INFO]    [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:36] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2026-04-28 23:42:36] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] 13774 rows after translation; translated 13226 `uniprot_entry` IDs in column `id_organism_b` to 13226 `uniprot` IDs in column `id_organism_b`.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Saving database `oma` to on-disk cache.
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:36] [INFO]    [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e0bb78c15459541ddf64018acdc4bad95c1fa369-1.rds`.
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Download ready [key=e0bb78c15459541ddf64018acdc4bad95c1fa369, version=1]
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Cache item `e0bb78c15459541ddf64018acdc4bad95c1fa369` version 1: status changed from `started` to `ready`.
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-04-28 23:42:37] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:42:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:42:38] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:42:38] [TRACE]   [OmnipathR] Downloaded 43 bytes in 1.597112s from rest.uniprot.org (26 bytes/s); Redirect: 0s, DNS look up: 0.001826s, Connection: 0.002529s, Pretransfer: 0.504138s, First byte at: 1.59706s
[2026-04-28 23:42:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:42:38 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:43:38] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-28 23:43:43] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:43:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:43:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:43:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:43:44] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:43:44] [TRACE]   [OmnipathR] Downloaded 43 bytes in 1.023071s from rest.uniprot.org (42 bytes/s); Redirect: 0s, DNS look up: 0.001549s, Connection: 0.002507s, Pretransfer: 0.499013s, First byte at: 1.023016s
[2026-04-28 23:43:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:43:44 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:44:44] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-28 23:44:49] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-04-28 23:44:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:44:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:44:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:44:51] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-04-28 23:44:51] [TRACE]   [OmnipathR] Downloaded 43 bytes in 1.213665s from rest.uniprot.org (35 bytes/s); Redirect: 0s, DNS look up: 0.001972s, Connection: 0.0028s, Pretransfer: 0.520752s, First byte at: 1.213616s
[2026-04-28 23:44:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 29 Apr 2026 03:44:51 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-04-28 23:47:20] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2026-04-28 23:47:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-28 23:47:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-04-28
[2026-04-28 23:47:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-28 19:28:53 UTC; unix
[2026-04-28 23:47:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 4.0.0
[2026-04-28 23:47:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-28 23:47:21] [INFO]    [OmnipathR] Session info: [version=R version 4.6.0 RC (2026-04-17 r89917); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-04-28; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-28 23:47:21] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-04-28 23:47:21] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.90.0(2026-04-28); AnnotationDbi 1.74.0(2026-04-28); AUCell 1.34.0(2026-04-28); backports 1.5.1(2026-04-03); beachmat 2.28.0(2026-04-28); Biobase 2.72.0(2026-04-28); BiocGenerics 0.58.0(2026-04-28); BiocParallel 1.46.0(2026-04-28); BiocSingular 1.28.0(2026-04-28); Biostrings 2.80.0(2026-04-28); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); broom 1.0.12(2026-01-27); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); class 7.3-23(2025-01-01); cli 3.6.6(2026-04-09); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.18.0(2026-04-28); DelayedArray 0.38.0(2026-04-28); DelayedMatrixStats 1.34.0(2026-04-28); desc 1.4.3(2023-12-10); diffobj 0.3.6(2025-04-21); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); e1071 1.7-17(2025-12-18); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.38.0(2026-04-28); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); GenomicRanges 1.64.0(2026-04-28); ggplot2 4.0.3(2026-04-22); glue 1.8.1(2026-04-17); graph 1.90.0(2026-04-28); GSEABase 1.74.0(2026-04-28); GSVA 2.6.0(2026-04-28); gtable 0.3.6(2024-10-25); h5mread 1.4.0(2026-04-28); HDF5Array 1.40.0(2026-04-28); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.0(2026-04-21); IRanges 2.46.0(2026-04-28); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.52.0(2026-04-28); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lazyeval 0.2.3(2026-04-04); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.1(2026-02-28); magrittr 2.0.5(2026-04-04); MASS 7.3-65(2025-02-28); Matrix 1.7-5(2026-03-21); MatrixGenerics 1.24.0(2026-04-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); mixtools 2.0.0.1(2025-03-08); nlme 3.1-169(2026-03-27); OmnipathR 4.0.0(2026-04-28); otel 0.2.0(2025-08-29); parallelly 1.47.0(2026-04-17); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-29(2025-12-29); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.18.0(2026-01-16); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.56.0(2026-04-28); rhdf5filters 1.24.0(2026-04-28); Rhdf5lib 2.0.0(2026-04-28); rjson 0.2.23(2024-09-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); rpart 4.1.27(2026-03-27); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.12.0(2026-04-28); S4Vectors 0.50.0(2026-04-28); S7 0.2.2(2026-04-22); ScaledMatrix 1.20.0(2026-04-28); scales 1.4.0(2025-04-24); segmented 2.2-1(2026-01-29); selectr 0.5-1(2025-12-17); Seqinfo 1.2.0(2026-04-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.34.0(2026-04-28); SparseArray 1.12.0(2026-04-28); sparseMatrixStats 1.24.0(2026-04-28); SpatialExperiment 1.22.0(2026-04-28); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.42.0(2026-04-28); survival 3.8-6(2026-01-16); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); viper 1.46.0(2026-04-28); viridisLite 0.4.3(2026-02-04); vroom 1.7.1(2026-03-31); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.52.0(2026-04-28); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-04-28 23:47:21] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
Saving _problems/test-omnipath-19.R
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C,D],organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:47:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:47:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:47:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.626517s from omnipathdb.org (25.1 Kb/s); Redirect: 0s, DNS look up: 0.178922s, Connection: 0.179776s, Pretransfer: 0.479291s, First byte at: 0.625514s
[2026-04-28 23:47:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:47:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:47:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:47:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:27] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:47:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-28 23:47:28] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-04-28 23:47:28] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2026-04-28 23:47:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:28] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2026-04-28 23:47:36] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C,D],organisms=10090,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.295898s from omnipathdb.org (53.1 Kb/s); Redirect: 0s, DNS look up: 0.001346s, Connection: 0.002567s, Pretransfer: 0.150052s, First byte at: 0.295182s
[2026-04-28 23:47:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:47:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:47:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:47:53] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-04-28 23:47:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:53] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:47:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-28 23:47:54] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-04-28 23:47:54] [INFO]    [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2026-04-28 23:47:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:47:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:47:54] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2026-04-28 23:48:01] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,loops=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:48:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:48:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:48:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.451023s from omnipathdb.org (34.8 Kb/s); Redirect: 0s, DNS look up: 0.001547s, Connection: 0.002437s, Pretransfer: 0.301172s, First byte at: 0.450514s
[2026-04-28 23:48:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:48:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:48:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:48:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:16] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-28 23:48:16] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:16] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-04-28 23:48:18] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:48:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=[evidences,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-04-28 23:48:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-04-28 23:48:20] [TRACE]   [OmnipathR] Downloaded 6.7 Kb in 0.233945s from omnipathdb.org (28.8 Kb/s); Redirect: 0s, DNS look up: 0.001315s, Connection: 0.002001s, Pretransfer: 0.1564s, First byte at: 0.233226s
[2026-04-28 23:48:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 29 Apr 2026 03:48:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Wed, 29 Apr 2026 04:48:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-04-28 23:48:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:21] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-28 23:48:21] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:21] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-28 23:48:21] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=collectri,types=<NULL>,genesymbols=TRUE,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,loops=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:48:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:22] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-04-28 23:48:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-04-28 23:48:24] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE]
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-04-28 23:48:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=CollecTRI,datasets=tf_mirna,types=<NULL>,genesymbols=TRUE,fields=[evidences,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=TRUE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-04-28 23:48:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-04-28 23:48:25] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-04-28 23:48:25] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%

Saving _problems/test-statistic-fgsea-26.R

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

[ FAIL 3 | WARN 9 | SKIP 0 | PASS 32 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-decoupleR-decouple.R:82:5'): decouple same results as independent functions ──
Expected `res_decouple_defaults` to equal `exp_decouple_defaults`.
Differences:
actual vs expected
                        p_value
  actual[214, ]    2.000000e-02
  actual[215, ]    6.000000e-02
  actual[216, ]    4.000000e-02
- actual[217, ]    1.048460e-01
+ expected[217, ]  7.547971e-02
- actual[218, ]    8.666012e-02
+ expected[218, ]  7.641156e-02
- actual[219, ]    1.185884e-01
+ expected[219, ]  1.142380e-01
- actual[220, ]    4.020773e-03
+ expected[220, ]  4.682543e-03
- actual[221, ]    1.309641e-01
+ expected[221, ]  1.412426e-01
- actual[222, ]    1.242426e-01
+ expected[222, ]  1.127250e-01
- actual[223, ]    9.243006e-02
+ expected[223, ]  1.036466e-01
and 44 more ...

actual vs expected
                        p_value
  actual[274, ]    1.000000e-02
  actual[275, ]    1.000000e-02
  actual[276, ]    1.000000e-02
- actual[277, ]    1.183552e-01
+ expected[277, ]  1.232047e-01
- actual[278, ]    1.290222e-01
+ expected[278, ]  1.724317e-01
- actual[279, ]    1.604518e-01
+ expected[279, ]  1.542813e-01
- actual[280, ]    5.779082e-03
+ expected[280, ]  5.020222e-03
- actual[281, ]    1.474283e-01
+ expected[281, ]  1.311256e-01
- actual[282, ]    1.388790e-01
+ expected[282, ]  2.139183e-01
- actual[283, ]    1.306695e-01
+ expected[283, ]  1.802104e-01
and 8 more ...

actual vs expected
                        p_value
  actual[502, ]    1.406126e-01
  actual[503, ]    2.966346e-01
  actual[504, ]    4.155902e-01
- actual[505, ]    1.048460e-01
+ expected[505, ]  7.547971e-02
- actual[506, ]    8.666012e-02
+ expected[506, ]  7.641156e-02
- actual[507, ]    1.185884e-01
+ expected[507, ]  1.142380e-01
- actual[508, ]    4.020773e-03
+ expected[508, ]  4.682543e-03
- actual[509, ]    1.309641e-01
+ expected[509, ]  1.412426e-01
- actual[510, ]    1.242426e-01
+ expected[510, ]  1.127250e-01
- actual[511, ]    9.243006e-02
+ expected[511, ]  1.036466e-01
and 44 more ...

actual vs expected
                        p_value
  actual[562, ]    1.000000e-02
  actual[563, ]    1.000000e-02
  actual[564, ]    1.000000e-02
- actual[565, ]    1.183552e-01
+ expected[565, ]  1.232047e-01
- actual[566, ]    1.290222e-01
+ expected[566, ]  1.724317e-01
- actual[567, ]    1.604518e-01
+ expected[567, ]  1.542813e-01
- actual[568, ]    5.779082e-03
+ expected[568, ]  5.020222e-03
- actual[569, ]    1.474283e-01
+ expected[569, ]  1.311256e-01
- actual[570, ]    1.388790e-01
+ expected[570, ]  2.139183e-01
- actual[571, ]    1.306695e-01
+ expected[571, ]  1.802104e-01
and 8 more ...

      actual$p_value | expected$p_value                
[214] 0.02           | 0.02             [214]          
[215] 0.06           | 0.06             [215]          
[216] 0.04           | 0.04             [216]          
[217] 0.10           - 0.08             [217]          
[218] 0.09           - 0.08             [218]          
[219] 0.12           - 0.11             [219]          
[220] 0.00           | 0.00             [220]          
[221] 0.13           - 0.14             [221]          
[222] 0.12           - 0.11             [222]          
[223] 0.09           - 0.10             [223]          
  ... ...              ...              and 44 more ...

      actual$p_value | expected$p_value               
[275] 0.01           | 0.01             [275]         
[276] 0.01           | 0.01             [276]         
[277] 0.12           | 0.12             [277]         
[278] 0.13           - 0.17             [278]         
[279] 0.16           - 0.15             [279]         
[280] 0.01           | 0.01             [280]         
[281] 0.15           - 0.13             [281]         
[282] 0.14           - 0.21             [282]         
[283] 0.13           - 0.18             [283]         
[284] 0.10           - 0.11             [284]         
  ... ...              ...              and 7 more ...

      actual$p_value | expected$p_value                
[502] 0.14           | 0.14             [502]          
[503] 0.30           | 0.30             [503]          
[504] 0.42           | 0.42             [504]          
[505] 0.10           - 0.08             [505]          
[506] 0.09           - 0.08             [506]          
[507] 0.12           - 0.11             [507]          
[508] 0.00           | 0.00             [508]          
[509] 0.13           - 0.14             [509]          
[510] 0.12           - 0.11             [510]          
[511] 0.09           - 0.10             [511]          
  ... ...              ...              and 44 more ...

      actual$p_value | expected$p_value               
[563] 0.01           | 0.01             [563]         
[564] 0.01           | 0.01             [564]         
[565] 0.12           | 0.12             [565]         
[566] 0.13           - 0.17             [566]         
[567] 0.16           - 0.15             [567]         
[568] 0.01           | 0.01             [568]         
[569] 0.15           - 0.13             [569]         
[570] 0.14           - 0.21             [570]         
[571] 0.13           - 0.18             [571]         
[572] 0.10           - 0.11             [572]         
  ... ...              ...              and 7 more ...

── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
<curl_error_http2_stream/curl_error/error/condition>
Error in `(function (con, what, n = 1L, size = NA_integer_, signed = TRUE, endian = .Platform$endian)  {     if (!endian %in% c("big", "little", "swap"))          stop("invalid 'endian' argument")     if (is.character(con)) {         con <- file(con, "rb")         on.exit(close(con))     }     swap <- endian != .Platform$endian     if (!is.character(what) || is.na(what) || length(what) != 1L || !any(what == c("numeric", "double", "integer", "int", "logical", "complex", "character", "raw")))          what <- typeof(what)     .Internal(readBin(con, what, n, size, signed, swap)) })(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x57419deba5a0>), raw(0), 131071L)`: Stream error in the HTTP/2 framing layer [rest.uniprot.org]:
HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Backtrace:
     ▆
  1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
  2. │ ├─... %>% ...
  3. │ └─decoupleR::get_resource("PROGENy", organism = organism)
  4. │   └─... %>% ...
  5. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
  6. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
  7. ├─dplyr::bind_rows(.)
  8. │ └─rlang::list2(...)
  9. ├─purrr::map(...)
 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 11. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 12. ├─dplyr::group_split(.)
 13. ├─dplyr::group_by(., pathway)
 14. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
 15. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
 16. ├─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
 17. ├─... %>% ...
 18. ├─OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
 19. │ └─... %>% ...
 20. ├─purrr::reduce2(...)
 21. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
 22. │   └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
 23. │     ├─... %>% ...
 24. │     └─OmnipathR:::id_translation_table(...)
 25. │       └─OmnipathR::uniprot_full_id_mapping_table(...)
 26. │         └─... %>% trim_and_distinct
 27. ├─OmnipathR:::ensure_character(., From, To)
 28. │ └─d %>% mutate(across(c(!!!cols), as.character))
 29. ├─dplyr::mutate(., across(c(!!!cols), as.character))
 30. ├─OmnipathR:::trim_and_distinct(.)
 31. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 32. ├─dplyr::distinct(.)
 33. ├─dplyr::mutate(., across(everything(), str_trim))
 34. ├─dplyr::filter(., !is.na(From) & !is.na(To))
 35. ├─tidyr::separate_rows(., To, sep = "[; ]")
 36. ├─tidyr::separate_rows(., From, sep = "[; ]")
 37. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To))
 38. ├─dplyr::rename(., From = 1, To = 2)
 39. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism)
 40. │ ├─... %T>% load_success()
 41. │ └─OmnipathR:::generic_downloader(...)
 42. │   ├─... %>% omnipath_cache_save(url = url, post = post)
 43. │   ├─rlang::exec(...)
 44. │   └─OmnipathR (local) `<fn>`(...)
 45. ├─OmnipathR:::load_success(.)
 46. │ └─from_cache %<>% if_null(data %>% is_from_cache)
 47. ├─OmnipathR:::if_null(., data %>% is_from_cache)
 48. │ └─value1 %>% is.null %>% if (value2) value1
 49. ├─data %>% is_from_cache
 50. ├─OmnipathR:::is_from_cache(.)
 51. │ └─obj %>% attr("origin") %>% ...
 52. └─OmnipathR::omnipath_cache_save(., url = url, post = post)
 53.   └─base::saveRDS(data, target_path)
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
Expected `res_1` to equal `exp_1`.
Differences:
actual vs expected
                      p_value
- actual[1, ]     0.104845953
+ expected[1, ]   0.075479709
- actual[2, ]     0.104845953
+ expected[2, ]   0.075479709
- actual[3, ]     0.519279295
+ expected[3, ]   0.548454870
- actual[4, ]     0.519279295
+ expected[4, ]   0.548454870
  actual[5, ]     0.010000000
  actual[6, ]     0.010000000
- actual[7, ]     0.086660121
+ expected[7, ]   0.076411558
- actual[8, ]     0.086660121
+ expected[8, ]   0.076411558
- actual[9, ]     1.000000000
+ expected[9, ]   0.976649086
- actual[10, ]    1.000000000
+ expected[10, ]  0.976649086
and 134 more ...

     actual$p_value | expected$p_value                 
 [1] 0.105          - 0.075            [1]             
 [2] 0.105          - 0.075            [2]             
 [3] 0.519          - 0.548            [3]             
 [4] 0.519          - 0.548            [4]             
 [5] 0.010          | 0.010            [5]             
 [6] 0.010          | 0.010            [6]             
 [7] 0.087          - 0.076            [7]             
 [8] 0.087          - 0.076            [8]             
 [9] 1.000          - 0.977            [9]             
[10] 1.000          - 0.977            [10]            
 ... ...              ...              and 134 more ...


[ FAIL 3 | WARN 9 | SKIP 0 | PASS 32 ]
Error:
! Test failures.
Execution halted

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

name	user	system	elapsed
check_corr	0.080	0.032	0.112
convert_f_defaults	0.026	0.006	0.033
decouple	0.001	0.000	0.001
dot-fit_preprocessing	0.021	0.006	0.028
extract_sets	0.024	0.002	0.026
filt_minsize	0.036	0.007	0.043
get_collectri	32.542	2.464	41.196
get_dorothea	23.423	1.121	26.230
get_profile_of	0.001	0.000	0.000
get_progeny	6.719	0.412	12.530
get_resource	1.141	0.071	2.979
get_toy_data	0.002	0.000	0.003
intersect_regulons	0.025	0.005	0.030
pipe	0.000	0.000	0.001
pivot_wider_profile	0.000	0.001	0.001
randomize_matrix	0.001	0.000	0.000
rename_net	0.039	0.003	0.041
run_aucell	8.420	1.809	10.166
run_consensus	1.850	0.426	2.255
run_fgsea	23.304	0.461	23.750
run_gsva	1.919	0.547	2.433
run_mdt	0.136	0.031	0.162
run_mlm	0.089	0.013	0.099
run_ora	0.490	0.054	0.536
run_udt	0.278	0.024	0.298
run_ulm	0.075	0.008	0.081
run_viper	0.786	0.159	0.937
run_wmean	0.697	0.050	0.737
run_wsum	0.706	0.034	0.741
show_methods	0.046	0.005	0.051
show_resources	0.132	0.007	0.828
tidyeval	0	0	0