Pau Badia-i-Mompel
| Snapshot Date: 2024-10-04 13:40 -0400 (Fri, 04 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: devel |
| git_last_commit: aa9e0db |
| git_last_commit_date: 2024-04-30 11:34:47 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-05 11:42 -0400 (Sat, 05 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4466 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4498 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4446 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4445 |
| 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 520/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: decoupleR |
| Version: 2.11.0 |
| 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_2.11.0.tar.gz |
| StartedAt: 2024-10-04 20:04:05 -0400 (Fri, 04 Oct 2024) |
| EndedAt: 2024-10-04 20:12:07 -0400 (Fri, 04 Oct 2024) |
| EllapsedTime: 482.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_2.11.0.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 ‘2.11.0’
* 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
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Contains 8 files.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-04 20:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:04:45] [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 24.501 0.464 27.884
run_fgsea 23.480 0.159 23.727
run_aucell 8.496 0.467 9.020
get_collectri 7.474 0.482 13.430
get_progeny 7.363 0.548 14.842
* 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.
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)
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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[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Contains 8 files.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-04 20:08:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:05] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-10-04 20:08:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:07] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-10-04 20:08:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:07] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-10-04 20:08:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:07] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-10-04 20:08:07] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-10-04 20:08:07] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-10-04 20:08:07] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-10-04 20:08:08] [TRACE] [OmnipathR] HTTP 200
[2024-10-04 20:08:08] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:08] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-04 20:08:08] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-04 20:08:08] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-10-04 20:08:08] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-10-04 20:08:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-04 20:08:09] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-10-04 20:08:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-10-04 20:08:10] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-10-04 20:08:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:11] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:08:11] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-10-04 20:08:11] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-10-04 20:08:11] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-10-04 20:08:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:11] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-10-04 20:08:11] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:20] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:08:20] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-04 20:08:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-04 20:08:23] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-10-04 20:08:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-10-04 20:08:23] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-10-04 20:08:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2024-10-04 20:08:27] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:08:27] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:08:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:08:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:30] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-10-04 20:08:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-10-04 20:08:30] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-10-04 20:08:32] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-10-04 20:08:32] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:08:32] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-10-04 20:08:32] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-04 20:08:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2024-10-04 20:09:02] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:09:02] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2024-10-04 20:09:02] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2024-10-04 20:09:02] [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`
[2024-10-04 20:09:02] [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`.
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:09:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:09:02] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2024-10-04 20:09:02] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-04 20:09:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-04 20:09:20] [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$\x84\xe8\xff\x9f\xff\xef\xff\xfd\xff\xff\xc7\xfe\xbf\xfe\xcf\xff\xfe\xaf\036\177&Λ\xae\xfa\x9f\xd3s\xb3\xfb\177ه}\xd4\xd5+uE\xe2\xe7\xe3J'
[2024-10-04 20:09:25] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-04 20:09:44] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\0\0\0\0\0\0\xff\\\xbd˖\xec \xaf\xa5\xdb\xde~\x8az\x840\xbe71\xbe.\xdfX\xb6#3";5\xaaQ\xcd:\x8d3N\xe7\xbc}i*\xfe\x95Lv/\xf3\033\x98\xc0\030\x84$\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'
[2024-10-04 20:09:49] [TRACE] [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2024-10-04 20:10:07] [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'
[2024-10-04 20:10:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2024-10-04 20:10:07] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:10:07] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:07] [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`
[2024-10-04 20:10:11] [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`
[2024-10-04 20:10:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:11] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:10:11] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-10-04 20:10:13] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2024-10-04 20:10:13] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2024-10-04 20:10:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:13] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2024-10-04 20:10:26] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-10-04 20:10:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2024-10-04 20:10:38] [TRACE] [OmnipathR] Organism(s): 10090
[2024-10-04 20:10:38] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:38] [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`
[2024-10-04 20:10:47] [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`
[2024-10-04 20:10:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:47] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:10:47] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-10-04 20:10:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2024-10-04 20:10:50] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2024-10-04 20:10:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:10:50] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2024-10-04 20:10:59] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-10-04 20:11:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-10-04 20:11:09] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:11:09] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:11:09] [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`
[2024-10-04 20:11:09] [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`
[2024-10-04 20:11:09] [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`
[2024-10-04 20:11:09] [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`
[2024-10-04 20:11:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-10-04 20:11:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-10-04 20:11:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-10-04 20:11:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-10-04 20:11:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:11] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:11:11] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-10-04 20:11:11] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-10-04 20:11:11] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2024-10-04 20:11:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:11] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2024-10-04 20:11:14] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-10-04 20:11:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-10-04 20:11:14] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:11:14] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:11:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [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`
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:15] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-10-04 20:11:15] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-04 20:11:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:15] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-10-04 20:11:15] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-10-04 20:11:16] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-10-04 20:11:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2024-10-04 20:11:16] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:11:16] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:11:16] [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`
[2024-10-04 20:11:16] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2024-10-04 20:11:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2024-10-04 20:11:19] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2024-10-04 20:11:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2024-10-04 20:11:19] [TRACE] [OmnipathR] Organism(s): 9606
[2024-10-04 20:11:19] [TRACE] [OmnipathR] Orthology targets:
[2024-10-04 20:11:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-10-04 20:11:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-04 20:11:20] [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`
[2024-10-04 20:11:20] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-10-04 20:11:20] [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`
[2024-10-04 20:11:20] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-10-04 20:11:20] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-10-04 20:11:20] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2024-10-04 20:11:21] [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
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.104 | 0.011 | 0.117 | |
| convert_f_defaults | 0.036 | 0.004 | 0.041 | |
| decouple | 0.001 | 0.001 | 0.002 | |
| dot-fit_preprocessing | 0.030 | 0.004 | 0.034 | |
| extract_sets | 0.030 | 0.001 | 0.031 | |
| filt_minsize | 0.055 | 0.001 | 0.058 | |
| get_collectri | 7.474 | 0.482 | 13.430 | |
| get_dorothea | 24.501 | 0.464 | 27.884 | |
| get_profile_of | 0.000 | 0.001 | 0.001 | |
| get_progeny | 7.363 | 0.548 | 14.842 | |
| get_resource | 0.390 | 0.036 | 1.959 | |
| get_toy_data | 0.002 | 0.000 | 0.002 | |
| intersect_regulons | 0.028 | 0.001 | 0.030 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| rename_net | 0.042 | 0.002 | 0.045 | |
| run_aucell | 8.496 | 0.467 | 9.020 | |
| run_consensus | 2.168 | 0.149 | 2.328 | |
| run_fgsea | 23.480 | 0.159 | 23.727 | |
| run_gsva | 1.748 | 0.175 | 1.934 | |
| run_mdt | 0.165 | 0.019 | 0.193 | |
| run_mlm | 0.099 | 0.001 | 0.101 | |
| run_ora | 0.611 | 0.010 | 0.623 | |
| run_udt | 0.366 | 0.019 | 0.386 | |
| run_ulm | 0.091 | 0.006 | 0.097 | |
| run_viper | 0.837 | 0.117 | 0.961 | |
| run_wmean | 0.859 | 0.008 | 0.870 | |
| run_wsum | 0.919 | 0.010 | 0.933 | |
| show_methods | 0.053 | 0.006 | 0.059 | |
| show_resources | 0.073 | 0.006 | 0.618 | |
| tidyeval | 0 | 0 | 0 | |