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This page was generated on 2023-03-27 05:50:32 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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CHECK results for decoupleR on kunpeng1


To the developers/maintainers of the decoupleR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 502/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.5.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: devel
git_last_commit: cb48916
git_last_commit_date: 2022-11-01 15:25:03 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    ERROR  

Summary

Package: decoupleR
Version: 2.5.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.5.0.tar.gz
StartedAt: 2023-03-25 00:45:04 -0000 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 00:56:13 -0000 (Sat, 25 Mar 2023)
EllapsedTime: 668.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Contains 6 files.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-25 00:45:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:45:35] [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 ... OK
* 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 29.252  0.809  31.854
run_fgsea    22.793  0.340  23.170
run_aucell    8.641  0.244   8.892
get_progeny   8.304  0.373  18.512
get_resource  0.667  0.036   8.760
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
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  Killed
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decoupleR.Rmd’ using ‘UTF-8’... OK
  ‘pw_bk.Rmd’ using ‘UTF-8’... OK
  ‘pw_sc.Rmd’ using ‘UTF-8’... OK
  ‘tf_bk.Rmd’ using ‘UTF-8’... OK
  ‘tf_sc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck/00check.log’
for details.

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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.fail


R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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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[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Contains 4 files.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:14] [TRACE]   [OmnipathR] Cache locked: FALSE
[2023-03-25 00:49:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-03-25 00:49:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-03-25 00:49:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:20] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-03-25 00:49:20] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-03-25 00:49:20] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-03-25 00:49:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:21] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-03-25 00:49:21] [SUCCESS] [OmnipathR] Downloaded 3516 annotation records.
[2023-03-25 00:49:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-25 00:49:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-25 00:49:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-25 00:49:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:34] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-03-25 00:49:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-03-25 00:49:37] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-03-25 00:49:37] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-03-25 00:49:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:37] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-03-25 00:49:37] [SUCCESS] [OmnipathR] Downloaded 700257 annotation records.
[2023-03-25 00:49:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-03-25 00:49:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-03-25 00:49:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-03-25 00:49:47] [SUCCESS] [OmnipathR] Loaded 700257 annotation records from cache.
[2023-03-25 00:49:51] [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`
[2023-03-25 00:49:51] [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`
[2023-03-25 00:49:51] [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`
[2023-03-25 00:49:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:55] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-03-25 00:49:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-03-25 00:49:56] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-03-25 00:49:56] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-03-25 00:49:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:49:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:49:56] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2023-03-25 00:50:09] [SUCCESS] [OmnipathR] Downloaded 278482 interactions.
[2023-03-25 00:50:23] [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`
[2023-03-25 00:50:23] [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`
[2023-03-25 00:50:23] [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`
[2023-03-25 00:50:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:50:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:50:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:50:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:50:26] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2023-03-25 00:50:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-03-25 00:50:27] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-03-25 00:50:27] [INFO]    [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2023-03-25 00:50:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-03-25 00:50:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-03-25 00:50:28] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2023-03-25 00:50:39] [SUCCESS] [OmnipathR] Downloaded 256977 interactions.

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Killed

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.1210.0080.129
convert_f_defaults0.1010.0000.101
decouple0.0010.0000.001
dot-fit_preprocessing0.0300.0000.031
extract_sets0.0330.0000.033
filt_minsize0.0570.0000.057
get_dorothea29.252 0.80931.854
get_profile_of000
get_progeny 8.304 0.37318.512
get_resource0.6670.0368.760
get_toy_data0.0030.0000.003
intersect_regulons0.0280.0000.029
pipe0.0000.0000.001
pivot_wider_profile000
randomize_matrix000
rename_net0.0450.0000.045
run_aucell8.6410.2448.892
run_consensus3.1550.1883.363
run_fgsea22.793 0.34023.170
run_gsva1.3180.1401.557
run_mdt0.3310.0200.357
run_mlm0.1720.0200.192
run_ora0.6770.0360.719
run_udt0.3820.0240.412
run_ulm0.2990.0040.303
run_viper0.8360.0600.928
run_wmean1.2490.0121.262
run_wsum1.2280.0121.241
show_methods0.0590.0040.065
show_resources0.2070.0041.558
tidyeval000