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This page was generated on 2024-05-04 11:40:26 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    TIMEOUT  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for decoupleR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: decoupleR
Version: 2.10.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings decoupleR_2.10.0.tar.gz
StartedAt: 2024-05-04 06:42:06 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 07:22:06 -0000 (Sat, 04 May 2024)
EllapsedTime: 2400.1 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings decoupleR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2024-05-04 06:42:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 06:42:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 06:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 06:42:51] [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  688.238 11.938 708.276
get_collectri 173.831  2.530 183.857
run_fgsea      25.268  0.671  26.004
get_progeny     8.669  0.814  17.835
run_aucell      8.844  0.634   9.500
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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

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

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

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

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[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:35] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-04 07:00:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:00:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:37] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:37] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:37] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-04 07:00:37] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-04 07:00:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] HTTP 200
[2024-05-04 07:00:40] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:40] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-04 07:00:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:41] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:00:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-04 07:00:41] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 07:00:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-05-04 07:00:43] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-04 07:00:43] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-05-04 07:00:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-05-04 07:00:43] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:45] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-04 07:00:45] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:45] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-05-04 07:00:45] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-05-04 07:00:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:00:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:00:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:56] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:00:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-04 07:00:59] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-04 07:00:59] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-05-04 07:00:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:00:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:00:59] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-05-04 07:00:59] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-05-04 07:01:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:01:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:01:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-04 07:01:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:01:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:01:06] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-04 07:01:06] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-04 07:01:06] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-05-04 07:01:09] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:09] [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`
[2024-05-04 07:01:19] [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`
[2024-05-04 07:01:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:01:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:01:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:01:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:01:19] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:01:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-04 07:01:21] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-04 07:01:21] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-05-04 07:01:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:01:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:01:21] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-05-04 07:01:22] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-04 07:01:46] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-04 07:02:17] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-04 07:12:45] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:12:59] [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`
[2024-05-04 07:13:04] [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`
[2024-05-04 07:13:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:13:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:13:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:13:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:13:04] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:13:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-04 07:13:06] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-04 07:13:06] [INFO]    [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-05-04 07:13:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:13:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:13:06] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-05-04 07:13:06] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-04 07:13:18] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-04 07:13:38] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-04 07:21:12] [SUCCESS] [OmnipathR] Downloaded 5294 interactions.
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:12] [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`
[2024-05-04 07:21:15] [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`
[2024-05-04 07:21:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:21:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:21:15] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-05-04 07:21:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-04 07:21:16] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-04 07:21:16] [INFO]    [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-05-04 07:21:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 07:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 07:21:16] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-05-04 07:21:16] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-04 07:21:22] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-05-04 07:21:28] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.0910.0160.108
convert_f_defaults0.0240.0120.036
decouple0.0010.0000.001
dot-fit_preprocessing0.0270.0000.029
extract_sets0.0280.0000.028
filt_minsize0.0500.0040.054
get_collectri173.831 2.530183.857
get_dorothea688.238 11.938708.276
get_profile_of000
get_progeny 8.669 0.81417.835
get_resource0.4180.0243.609
get_toy_data0.0030.0000.003
intersect_regulons0.0310.0000.031
pipe0.0010.0000.000
pivot_wider_profile000
randomize_matrix000
rename_net0.0470.0000.047
run_aucell8.8440.6349.500
run_consensus2.6070.0802.694
run_fgsea25.268 0.67126.004
run_gsva1.7360.0471.791
run_mdt0.1700.0260.189
run_mlm0.1050.0160.121
run_ora0.6180.0160.635
run_udt0.3790.0160.396
run_ulm0.0820.0120.094
run_viper0.8190.0520.873
run_wmean1.0700.0521.124
run_wsum0.9820.0120.996
show_methods0.0710.0000.072
show_resources0.0810.0121.342
tidyeval0.0000.0000.001