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This page was generated on 2024-05-09 11:40:45 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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: 2024-05-08 14:00:19 -0400 (Wed, 08 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    ERROR  skippedskipped
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: 2024-05-09 06:35:27 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 07:15:27 -0000 (Thu, 09 May 2024)
EllapsedTime: 2400.2 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
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 06:36:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:11] [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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_collectri
> ### Title: CollecTRI gene regulatory network. Wrapper to access CollecTRI
> ###   gene regulatory network. CollecTRI is a comprehensive resource
> ###   containing a curated collection of transcription factors (TFs) and
> ###   their target genes. It is an expansion of DoRothEA. Each interaction
> ###   is weighted by its mode of regulation (either positive or negative).
> ### Aliases: get_collectri
> 
> ### ** Examples
> 
> collectri <- get_collectri(organism='human', split_complexes=FALSE)
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-09 06:36:46] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:36:46] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-09 06:36:46] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:36:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:39:49] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:39:49] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-05-09 06:39:54] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:43:00] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:43:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-05-09 06:43:05] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:46:08] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:46:08] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-05-09 06:46:08] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-09 06:46:08] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-09 06:46:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:46:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:46:08] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-05-09 06:46:08] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-05-09 06:46:08] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:46:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:49:15] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:49:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-05-09 06:49:20] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:52:23] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:52:23] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-05-09 06:52:28] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:55:31] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 06:55:31] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-05-09 06:55:31] [WARN]    [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2024-05-09 06:55:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:31] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:31] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:31] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:35] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:55:35] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-05-09 06:55:35] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:55:35] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-05-09 06:55:35] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-09 06:55:42] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
Calls: get_collectri ... tidyselect_data_has_predicates -> unnest_evidences -> %>%
Execution halted
* 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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[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Contains 4 files.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:00] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-09 06:57:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-09 06:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 06:57:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-09 06:57:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 06:57:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:00:06] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 07:00:06] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-05-09 07:00:11] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:03:13] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 07:03:13] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-05-09 07:03:18] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:06:27] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 07:06:27] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-05-09 07:06:27] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-09 07:06:27] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-09 07:06:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 07:06:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 07:06:27] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-05-09 07:06:27] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-05-09 07:06:27] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:06:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:09:29] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 07:09:29] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-05-09 07:09:34] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-09 07:12:39] [WARN]    [OmnipathR] HTTP 404
[2024-05-09 07:12:39] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-05-09 07:12:44] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.1010.0080.110
convert_f_defaults0.0370.0000.037
decouple0.0010.0000.001
dot-fit_preprocessing0.0290.0000.030
extract_sets0.0290.0000.029
filt_minsize0.0530.0000.053