Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:39:05 -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 lconway


To the developers/maintainers of the decoupleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: decoupleR
Version: 2.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.10.0.tar.gz
StartedAt: 2024-05-03 21:20:42 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:58:53 -0400 (Fri, 03 May 2024)
EllapsedTime: 2290.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: decoupleR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* 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 dependencies in R code ... NOTE
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 21:21:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 21:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 21:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:21:23] [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  550.951  7.293 588.626
get_collectri 134.783  1.945 150.438
run_fgsea      22.020  0.370  22.564
run_aucell      9.858  1.205  11.187
get_progeny     6.375  0.589  14.539
* 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:
   35. │ │ ├─enquo(arg) %>% ...
   36. │ │ └─rlang::enquo(arg)
   37. │ └─rlang::enquo(organism)
   38. ├─OmnipathR::ncbi_taxid(.)
   39. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
   40. ├─purrr::map_int(., taxon_name, "ncbi")
   41. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
   42. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
   43. └─rlang::sym(organism_b)
   44.   └─rlang:::abort_coercion(x, "a symbol")
   45.     └─rlang::abort(msg, call = call)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck/00check.log’
for details.


Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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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[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:28] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:36:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:30] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:30] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:36:30] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-05-03 21:36:30] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-05-03 21:36:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] HTTP 200
[2024-05-03 21:37:29] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:29] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-03 21:37:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-03 21:37:29] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-05-03 21:37:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:32] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-05-03 21:37:32] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:32] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-05-03 21:37:32] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-05-03 21:37:33] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:37:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:42] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:37:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-03 21:37:45] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-03 21:37:45] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-05-03 21:37:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:37:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:45] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-05-03 21:37:45] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-05-03 21:37:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:37:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:37:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:51] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-05-03 21:37:51] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-05-03 21:37:51] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-05-03 21:37:54] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:37:54] [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`
[2024-05-03 21:38:04] [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`
[2024-05-03 21:38:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:38:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:38:04] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:38:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-03 21:38:07] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-05-03 21:38:07] [INFO]    [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-05-03 21:38:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:38:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:38:07] [INFO]    [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-05-03 21:38:07] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:38:30] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-03 21:38:53] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-03 21:46:57] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:08] [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`
[2024-05-03 21:47:13] [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`
[2024-05-03 21:47:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:47:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:47:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:47:13] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:47:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-03 21:47:15] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-05-03 21:47:15] [INFO]    [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-05-03 21:47:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:47:15] [INFO]    [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-05-03 21:47:15] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:47:26] [TRACE]   [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-05-03 21:47:39] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none
[2024-05-03 21:53:35] [SUCCESS] [OmnipathR] Downloaded 5294 interactions.
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:35] [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`
[2024-05-03 21:53:40] [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`
[2024-05-03 21:53:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:53:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:53:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:53:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:53:40] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:53:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-03 21:53:41] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-03 21:53:41] [INFO]    [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-05-03 21:53:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:53:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:53:41] [INFO]    [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-05-03 21:53:41] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:53:46] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-05-03 21:53:51] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none
[2024-05-03 21:55:49] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:55:50] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:55:50] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-05-03 21:55:51] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-05-03 21:55:51] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-05-03 21:55:51] [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`
[2024-05-03 21:55:52] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-05-03 21:55:52] [INFO]    [OmnipathR] Loaded from 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`
[2024-05-03 21:55:52] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:55:57] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-05-03 21:56:02] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none
[2024-05-03 21:58:04] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-05-03 21:58:04] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-05-03 21:58:04] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-05-03 21:58:05] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-05-03 21:58:05] [SUCCESS] [OmnipathR] Downloaded 232 interactions.

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Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 34 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
Error in `sym(organism_b)`: Can't convert an integer vector to a symbol.
Backtrace:
     ▆
  1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
  2. │ ├─... %>% ...
  3. │ └─decoupleR::get_resource("PROGENy", organism = organism)
  4. │   └─... %>% ...
  5. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
  6. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
  7. ├─dplyr::bind_rows(.)
  8. │ └─rlang::list2(...)
  9. ├─purrr::map(...)
 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 11. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 12. ├─dplyr::group_split(.)
 13. ├─dplyr::group_by(., pathway)
 14. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
 15. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
 16. ├─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
 17. ├─... %>% ...
 18. ├─OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
 19. ├─OmnipathR::orthology_translate_column(...)
 20. │ ├─... %>% ...
 21. │ └─OmnipathR::get_db(db_name, param = orthology_param)
 22. │   └─OmnipathR::load_db(key, param = param)
 23. │     ├─rlang::exec(loader, !!!param)
 24. │     └─OmnipathR (local) `<fn>`(organism_a = 9606L, organism_b = 10090L)
 25. │       └─environment() %>% as.list %>% ...
 26. ├─rlang::set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
 27. ├─dplyr::select(., -any_of("hgroup"))
 28. ├─rlang::exec(oma_pairwise_translated, !!!.)
 29. ├─OmnipathR (local) `<fn>`(...)
 30. │ └─... %>% ...
 31. ├─dplyr::filter(., !is.na(id_organism_a) & !is.na(id_organism_b))
 32. ├─OmnipathR::translate_ids(...)
 33. │ ├─... %>% ncbi_taxid
 34. │ ├─OmnipathR:::.nse_ensure_str(!!enquo(organism))
 35. │ │ ├─enquo(arg) %>% ...
 36. │ │ └─rlang::enquo(arg)
 37. │ └─rlang::enquo(organism)
 38. ├─OmnipathR::ncbi_taxid(.)
 39. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 40. ├─purrr::map_int(., taxon_name, "ncbi")
 41. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 42. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
 43. └─rlang::sym(organism_b)
 44.   └─rlang:::abort_coercion(x, "a symbol")
 45.     └─rlang::abort(msg, call = call)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.0970.0110.109
convert_f_defaults0.0340.0050.040
decouple0.0010.0010.001
dot-fit_preprocessing0.0270.0040.031
extract_sets0.0290.0020.032
filt_minsize0.0510.0020.055
get_collectri134.783 1.945150.438
get_dorothea550.951 7.293588.626
get_profile_of0.0000.0010.001
get_progeny 6.375 0.58914.539
get_resource0.4010.0402.338
get_toy_data0.0020.0000.002
intersect_regulons0.0290.0010.031
pipe000
pivot_wider_profile0.0010.0010.001
randomize_matrix000
rename_net0.0400.0010.042
run_aucell 9.858 1.20511.187
run_consensus2.0500.0232.087
run_fgsea22.020 0.37022.564
run_gsva1.6810.1701.874
run_mdt0.1520.0230.181
run_mlm0.1070.0020.110
run_ora0.5590.0070.571
run_udt0.3350.0080.346
run_ulm0.0860.0020.091
run_viper0.7830.1220.915
run_wmean0.9410.0230.973
run_wsum0.8670.0120.888
show_methods0.0520.0060.059
show_resources0.0640.0060.677
tidyeval0.0010.0000.000