Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 522/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.12.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_20
git_last_commit: bc3245c
git_last_commit_date: 2024-10-29 11:00:29 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for decoupleR on palomino8

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: 2.12.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decoupleR_2.12.0.tar.gz
StartedAt: 2024-12-20 00:42:57 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:52:00 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 543.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: decoupleR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decoupleR_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '2.12.0'
* 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
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:36] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Contains 8 files.
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:43:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:37] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-20 00:43:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:43:37] [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  24.84   0.35   25.30
run_fgsea     23.54   0.03   23.58
run_aucell     8.42   0.61    9.05
get_progeny    7.30   0.42    9.06
get_collectri  6.80   0.64   11.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck/00check.log'
for details.


Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
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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[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Contains 8 files.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:42] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-12-20 00:48:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-12-20 00:48:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] HTTP 200
[2024-12-20 00:48:44] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:44] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-12-20 00:48:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:44] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-12-20 00:48:44] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-12-20 00:48:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-12-20 00:48:45] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-12-20 00:48:45] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-12-20 00:48:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:45] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-12-20 00:48:45] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:46] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:48:46] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-12-20 00:48:47] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:47] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-12-20 00:48:47] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:48:47] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:50] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:48:50] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-12-20 00:48:53] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-12-20 00:48:53] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-12-20 00:48:53] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:48:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:53] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-12-20 00:48:53] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:48:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:59] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-12-20 00:48:59] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-12-20 00:48:59] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-12-20 00:49:02] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-12-20 00:49:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:02] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-12-20 00:49:02] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-12-20 00:49:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-12-20 00:49:28] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:28] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-12-20 00:49:28] [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`
[2024-12-20 00:49:28] [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`.
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:28] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-12-20 00:49:28] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-12-20 00:49:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-12-20 00:49:45] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-12-20 00:49:45] [INFO]    [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2024-12-20 00:49:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:45] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2024-12-20 00:49:45] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] 13774 rows after translation; translated 13573 `uniprot_entry` IDs in column `id_organism_a` to 13573 `uniprot` IDs in column `id_organism_a`.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2024-12-20 00:49:46] [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`
[2024-12-20 00:49:46] [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`.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:46] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2024-12-20 00:49:46] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2024-12-20 00:49:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2024-12-20 00:49:56] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2024-12-20 00:49:56] [INFO]    [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2024-12-20 00:49:56] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:56] [INFO]    [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2024-12-20 00:49:56] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17229 records
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] 13774 rows after translation; translated 13276 `uniprot_entry` IDs in column `id_organism_b` to 13276 `uniprot` IDs in column `id_organism_b`.
[2024-12-20 00:49:57] [INFO]    [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2024-12-20 00:49:57] [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`.
[2024-12-20 00:49:57] [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`
[2024-12-20 00:49:57] [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`.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:49:57] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-12-20 00:49:57] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-12-20 00:49:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-12-20 00:50:07] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-12-20 00:50:07] [INFO]    [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2024-12-20 00:50:07] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:07] [INFO]    [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2024-12-20 00:50:07] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17229 records
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] 164220 rows before translation, 12880 uniprot IDs in column `uniprot`.
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] 164220 rows after translation; translated 12880 `uniprot` IDs in column `uniprot` to 12791 `genesymbol` IDs in column `genesymbol`.
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:50:08] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:08] [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`
[2024-12-20 00:50:10] [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`
[2024-12-20 00:50:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:10] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:50:10] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-12-20 00:50:12] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-12-20 00:50:12] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2024-12-20 00:50:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:12] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2024-12-20 00:50:23] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Organism(s): 10090
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-12-20 00:50:37] [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`
[2024-12-20 00:50:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:37] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:50:37] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-12-20 00:50:38] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-12-20 00:50:38] [INFO]    [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2024-12-20 00:50:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:38] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2024-12-20 00:50:47] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-12-20 00:50:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-12-20 00:50:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:50:58] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:50:58] [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`
[2024-12-20 00:50:58] [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`
[2024-12-20 00:50:58] [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`
[2024-12-20 00:50:58] [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`
[2024-12-20 00:50:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-12-20 00:50:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-12-20 00:50:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-12-20 00:50:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:59] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-12-20 00:50:59] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:50:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:50:59] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2024-12-20 00:51:02] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-12-20 00:51:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-12-20 00:51:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:51:02] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [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`
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:51:03] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-12-20 00:51:03] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:51:03] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-12-20 00:51:03] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-12-20 00:51:04] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-12-20 00:51:04] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-12-20 00:51:04] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:51:04] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:51:04] [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`
[2024-12-20 00:51:05] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-12-20 00:51:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-12-20 00:51:08] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Orthology targets: 
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 00:51:08] [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`
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-12-20 00:51:08] [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`
[2024-12-20 00:51:08] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-12-20 00:51:09] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-12-20 00:51:09] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-12-20 00:51:09] [SUCCESS] [OmnipathR] Downloaded 232 interactions.

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Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 189.23    4.90  363.15 

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.080.070.14
convert_f_defaults0.050.010.06
decouple000
dot-fit_preprocessing0.030.000.04
extract_sets0.010.000.01
filt_minsize0.050.000.05
get_collectri 6.80 0.6411.23
get_dorothea24.84 0.3525.30
get_profile_of000
get_progeny7.300.429.06
get_resource0.370.001.80
get_toy_data000
intersect_regulons0.030.010.05
pipe000
pivot_wider_profile000
randomize_matrix000
rename_net0.050.000.04
run_aucell8.420.619.05
run_consensus2.180.192.36
run_fgsea23.54 0.0323.58
run_gsva1.850.551.83
run_mdt0.230.140.18
run_mlm0.130.030.08
run_ora0.750.240.66
run_udt0.310.030.34
run_ulm0.090.010.11
run_viper0.910.101.00
run_wmean0.950.061.02
run_wsum0.890.010.90
show_methods0.080.000.08
show_resources0.080.000.48
tidyeval000