Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 527/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.10.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_19
git_last_commit: 7e6c106
git_last_commit_date: 2024-04-30 11:34:47 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  


CHECK results for decoupleR on palomino3

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: 2.10.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings decoupleR_2.10.0.tar.gz
StartedAt: 2024-06-13 02:36:54 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 03:16:55 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 2400.7 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings decoupleR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'decoupleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decoupleR' version '2.10.0'
* 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 whether package 'decoupleR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:54] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Contains 8 files.
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:37:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:54] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-13 02:37:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:37:55] [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 or links in Rd file 'run_gsva.Rd':
  'GSVA::gsva' 'GeneSetCollection'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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_dorothea  545.62  10.22  555.21
get_collectri 134.46   2.84  140.15
run_fgsea      21.63   0.69   22.34
run_aucell      7.83   2.61   10.61
get_progeny     7.58   0.50    9.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'decoupleR' ...
** 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


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

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

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

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[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:44] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Contains 8 files.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:44] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-13 02:55:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:46] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:46] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:46] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-06-13 02:55:46] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-06-13 02:55:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] HTTP 200
[2024-06-13 02:55:47] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:47] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-13 02:55:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:47] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-06-13 02:55:47] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-06-13 02:55:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-06-13 02:55:48] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-06-13 02:55:48] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-06-13 02:55:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:48] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-06-13 02:55:48] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:49] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-06-13 02:55:49] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:55:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:54] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:55:54] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-06-13 02:55:56] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-06-13 02:55:56] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-06-13 02:55:56] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:55:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:55:56] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-06-13 02:55:56] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-06-13 02:55:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:55:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-06-13 02:56:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:56:01] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-06-13 02:56:01] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-06-13 02:56:01] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-06-13 02:56:03] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-06-13 02:56:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:03] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-06-13 02:56:03] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-06-13 02:56:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-06-13 02:56:29] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:29] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-06-13 02:56:29] [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`
[2024-06-13 02:56:29] [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`.
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:56:29] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-06-13 02:56:29] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-06-13 02:56:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-06-13 02:57:51] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-06-13 02:57:51] [INFO]    [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2024-06-13 02:57:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:57:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:57:51] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2024-06-13 02:57:51] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20435 records
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2024-06-13 02:57:52] [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`
[2024-06-13 02:57:52] [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`.
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:57:52] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2024-06-13 02:57:52] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2024-06-13 02:57:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2024-06-13 02:59:51] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2024-06-13 02:59:51] [INFO]    [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2024-06-13 02:59:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:59:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:59:51] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2024-06-13 02:59:51] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17212 records
[2024-06-13 02:59:52] [INFO]    [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2024-06-13 02:59:52] [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`.
[2024-06-13 02:59:52] [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`
[2024-06-13 02:59:52] [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`.
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 02:59:52] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-06-13 02:59:52] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-06-13 02:59:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-06-13 03:02:04] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-06-13 03:02:04] [INFO]    [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2024-06-13 03:02:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:02:04] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2024-06-13 03:02:04] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17212 records
[2024-06-13 03:02:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:04] [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=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:05] [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=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:02:25] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:02:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:02:25] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:02:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:02:25] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-06-13 03:02:25] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-06-13 03:02:28] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-06-13 03:02:28] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-06-13 03:02:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:02:28] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-06-13 03:02:28] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-13 03:02:51] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-06-13 03:03:12] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-06-13 03:10:44] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-06-13 03:10:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [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=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [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=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:58] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-06-13 03:10:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:10:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:10:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:10:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:10:58] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-06-13 03:10:58] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-06-13 03:11:00] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-06-13 03:11:00] [INFO]    [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-06-13 03:11:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:11:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:11:00] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-06-13 03:11:00] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-13 03:11:11] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-06-13 03:11:24] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-06-13 03:16:41] [SUCCESS] [OmnipathR] Downloaded 5294 interactions.
[2024-06-13 03:16:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-06-13 03:16:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:16:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:16:46] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-06-13 03:16:46] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-06-13 03:16:47] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-06-13 03:16:47] [INFO]    [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-06-13 03:16:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 03:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 03:16:47] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-06-13 03:16:47] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-06-13 03:16:51] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.070.050.11
convert_f_defaults0.040.000.05
decouple000
dot-fit_preprocessing0.020.000.02
extract_sets0.010.000.01
filt_minsize0.030.020.05
get_collectri134.46 2.84140.15
get_dorothea545.62 10.22555.21
get_profile_of000
get_progeny7.580.509.58
get_resource0.510.132.39
get_toy_data000
intersect_regulons0.040.000.06
pipe000
pivot_wider_profile000
randomize_matrix000
rename_net0.060.000.06
run_aucell 7.83 2.6110.61
run_consensus1.680.061.74
run_fgsea21.63 0.6922.34
run_gsva1.670.812.11
run_mdt0.280.130.20
run_mlm0.110.050.08
run_ora0.630.180.53
run_udt0.280.040.31
run_ulm0.120.000.13
run_viper0.990.482.78
run_wmean2.280.052.50
run_wsum1.050.011.15
show_methods0.060.020.50
show_resources0.080.000.50
tidyeval000