Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (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

Package 522/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decoupleR 2.12.0  (landing page)
Pau Badia-i-Mompel
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/decoupleR
git_branch: RELEASE_3_20
git_last_commit: bc3245c
git_last_commit_date: 2024-10-29 11:00:29 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    TIMEOUT  


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: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2024-11-19 21:16:41 -0500 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 21:28:47 -0500 (Tue, 19 Nov 2024)
EllapsedTime: 726.5 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/decoupleR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Contains 8 files.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:20:52] [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
run_fgsea     19.433  0.158  19.696
get_dorothea  18.308  0.457  21.442
run_aucell     6.870  0.404   7.319
get_progeny    6.273  0.538  14.615
get_collectri  5.143  0.345  10.702
* 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:
   55. │   ├─rlang::exec(...)
   56. │   └─OmnipathR (local) `<fn>`(...)
   57. ├─OmnipathR:::load_success(.)
   58. │ └─from_cache %<>% if_null(data %>% is_from_cache)
   59. ├─OmnipathR:::if_null(., data %>% is_from_cache)
   60. │ └─value1 %>% is.null %>% if (value2) value1
   61. ├─data %>% is_from_cache
   62. ├─OmnipathR:::is_from_cache(.)
   63. │ └─obj %>% attr("origin") %>% ...
   64. └─OmnipathR::omnipath_cache_save(., url = url, post = post)
   65.   └─base::saveRDS(data, target_path)
  
  [ FAIL 1 | WARN 9 | 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-3.20-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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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[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:38] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Contains 8 files.
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:40] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:40] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:40] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-19 21:23:40] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-19 21:23:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-19 21:23:41] [TRACE]   [OmnipathR] HTTP 200
[2024-11-19 21:23:41] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-11-19 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:42] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-19 21:23:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:42] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-19 21:23:42] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-11-19 21:23:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-19 21:23:43] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-11-19 21:23:43] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:23:43] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:44] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-11-19 21:23:45] [INFO]    [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:45] [INFO]    [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-11-19 21:23:45] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:23:45] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:54] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:23:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-11-19 21:23:57] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-11-19 21:23:57] [INFO]    [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-11-19 21:23:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:23:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:23:57] [INFO]    [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-11-19 21:23:57] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-11-19 21:24:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:24:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-11-19 21:24:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:24:01] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:24:02] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:24:05] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-11-19 21:24:05] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-11-19 21:24:05] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-11-19 21:24:06] [INFO]    [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-11-19 21:24:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:07] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-11-19 21:24:07] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-11-19 21:24:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-11-19 21:24:34] [INFO]    [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:34] [INFO]    [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-11-19 21:24:34] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:24:34] [INFO]    [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-11-19 21:24:34] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-19 21:24:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-19 21:24:57] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-11-19 21:25:02] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-19 21:25:27] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-11-19 21:25:32] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-11-19 21:27:22] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [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=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [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=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:26] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:27:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-11-19 21:27:27] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-11-19 21:27:27] [INFO]    [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2024-11-19 21:27:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:27] [INFO]    [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2024-11-19 21:27:34] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Organism(s): 10090
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [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=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [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=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2024-11-19 21:27:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:52] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:27:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-11-19 21:27:53] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-11-19 21:27:53] [INFO]    [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2024-11-19 21:27:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:27:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:27:53] [INFO]    [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2024-11-19 21:27:59] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:07] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:28:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-11-19 21:28:08] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-11-19 21:28:08] [INFO]    [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2024-11-19 21:28:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:08] [INFO]    [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2024-11-19 21:28:09] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-11-19 21:28:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [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`
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:10] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-11-19 21:28:10] [INFO]    [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:10] [INFO]    [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-11-19 21:28:10] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-11-19 21:28:11] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-11-19 21:28:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-11-19 21:28:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:28:11] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:28:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:11] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-11-19 21:28:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-11-19 21:28:13] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2024-11-19 21:28:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-11-19 21:28:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-19 21:28:13] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:28:14] [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`
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-11-19 21:28:14] [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`
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-11-19 21:28:14] [TRACE]   [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-11-19 21:28:14] [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 9 | SKIP 0 | PASS 34 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
Error in `vroom_(file, delim = delim %||% col_types$delim, col_names = col_names, 
    col_types = col_types, id = id, skip = skip, col_select = col_select, 
    name_repair = .name_repair, na = na, quote = quote, trim_ws = trim_ws, 
    escape_double = escape_double, escape_backslash = escape_backslash, 
    comment = comment, skip_empty_rows = skip_empty_rows, locale = locale, 
    guess_max = guess_max, n_max = n_max, altrep = vroom_altrep(altrep), 
    num_threads = num_threads, progress = progress)`: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
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. ├─OmnipathR::translate_ids(...)
 34. │ └─d %<>% ...
 35. ├─purrr::reduce2(...)
 36. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
 37. │   └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
 38. │     ├─... %>% ...
 39. │     └─OmnipathR:::id_translation_table(...)
 40. │       └─OmnipathR::uniprot_full_id_mapping_table(...)
 41. │         └─... %>% trim_and_distinct
 42. ├─OmnipathR:::trim_and_distinct(.)
 43. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 44. ├─dplyr::distinct(.)
 45. ├─dplyr::mutate(., across(everything(), str_trim))
 46. ├─dplyr::filter(., !is.na(From) & !is.na(To))
 47. ├─tidyr::separate_rows(., To, sep = "[; ]")
 48. ├─tidyr::separate_rows(., From, sep = "[; ]")
 49. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To))
 50. ├─dplyr::rename(., From = 1, To = 2)
 51. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism)
 52. │ ├─... %T>% load_success()
 53. │ └─OmnipathR:::generic_downloader(...)
 54. │   ├─... %>% omnipath_cache_save(url = url, post = post)
 55. │   ├─rlang::exec(...)
 56. │   └─OmnipathR (local) `<fn>`(...)
 57. ├─OmnipathR:::load_success(.)
 58. │ └─from_cache %<>% if_null(data %>% is_from_cache)
 59. ├─OmnipathR:::if_null(., data %>% is_from_cache)
 60. │ └─value1 %>% is.null %>% if (value2) value1
 61. ├─data %>% is_from_cache
 62. ├─OmnipathR:::is_from_cache(.)
 63. │ └─obj %>% attr("origin") %>% ...
 64. └─OmnipathR::omnipath_cache_save(., url = url, post = post)
 65.   └─base::saveRDS(data, target_path)

[ FAIL 1 | WARN 9 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

nameusersystemelapsed
check_corr0.0740.0100.085
convert_f_defaults0.0230.0030.026
decouple0.0000.0000.001
dot-fit_preprocessing0.0190.0020.022
extract_sets0.0170.0010.018
filt_minsize0.0360.0010.037
get_collectri 5.143 0.34510.702
get_dorothea18.308 0.45721.442
get_profile_of0.0010.0010.000
get_progeny 6.273 0.53814.615
get_resource0.2810.0272.021
get_toy_data0.0030.0000.002
intersect_regulons0.0240.0010.025
pipe000
pivot_wider_profile0.0000.0000.001
randomize_matrix000
rename_net0.0360.0010.037
run_aucell6.8700.4047.319
run_consensus1.8730.1542.042
run_fgsea19.433 0.15819.696
run_gsva1.4080.1521.570
run_mdt0.1380.0230.170
run_mlm0.0830.0020.086
run_ora0.4490.0050.458
run_udt0.2410.0120.255
run_ulm0.0640.0040.068
run_viper0.6380.1050.754
run_wmean0.6450.0070.654
run_wsum0.7140.0100.729
show_methods0.0550.0070.063
show_resources0.0530.0040.678
tidyeval000