Multiple platform build/check report for BioC 3.20 - CHECK results for decoupleR on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4481
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4479
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4359
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4539
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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*

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: 2.12.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.12.0.tar.gz

StartedAt: 2024-11-20 06:57:34 -0000 (Wed, 20 Nov 2024)

EndedAt: 2024-11-20 07:37:34 -0000 (Wed, 20 Nov 2024)

EllapsedTime: 2400.1 seconds

RetCode: None

Status: TIMEOUT

CheckDir: decoupleR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘2.12.0’
* 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 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
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Contains 8 files.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 06:58:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:22] [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)
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-11-20 06:58:58] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:58:58] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-20 06:58:58] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 06:58:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:02:00] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:02:00] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 07:02:05] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:05:07] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:05:07] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 07:05:12] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:08:13] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:08:13] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 07:08:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-11-20 07:08:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 07:08:14] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 07:08:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:08:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:08:14] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-11-20 07:08:14] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-11-20 07:08:14] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:08:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:11:15] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:11:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 07:11:20] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:14:22] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:14:22] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 07:14:27] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:17:28] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:17:28] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 07:17:28] [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.
[2024-11-20 07:17:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:29] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:29] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:29] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:32] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2024-11-20 07:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:17:32] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2024-11-20 07:17:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-11-20 07:17:33] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2024-11-20 07:17:33] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2024-11-20 07:17:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:17:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:17:33] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2024-11-20 07:17:33] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-11-20 07:17:39] [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/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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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[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Contains 4 files.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:01] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-11-20 07:19:02] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-20 07:19:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:03] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:03] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:19:03] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-20 07:19:03] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:19:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:22:05] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:22:05] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 07:22:10] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:25:11] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:25:11] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 07:25:16] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:28:17] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:28:17] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 07:28:17] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2024-11-20 07:28:17] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 07:28:17] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 07:28:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:28:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:28:17] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2024-11-20 07:28:18] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2024-11-20 07:28:18] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:28:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:31:19] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:31:19] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404
[2024-11-20 07:31:24] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:34:26] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:34:26] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404
[2024-11-20 07:34:31] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:37:32] [WARN]    [OmnipathR] HTTP 404
[2024-11-20 07:37:32] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404
[2024-11-20 07:37:33] [WARN]    [OmnipathR] Accessing `TFcensus` 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.
[2024-11-20 07:37:33] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `TFcensus` from OmniPath. For more information, see the OmnipathR log.
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:37:34] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-20 07:37:34] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:37:34] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2024-11-20 07:37:34] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-20 07:37:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

name	user	system	elapsed
check_corr	0.095	0.016	0.112
convert_f_defaults	0.031	0.004	0.035
decouple	0.000	0.000	0.001
dot-fit_preprocessing	0.029	0.000	0.030
extract_sets	0.029	0.000	0.029
filt_minsize	0.057	0.008	0.064