| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:16 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 518/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.8.2 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | ERROR | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | ERROR | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.8.2 |
| 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_2.8.2.tar.gz |
| StartedAt: 2024-03-03 20:04:27 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 20:32:23 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 1676.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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_2.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.8.2’
* 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 ... NOTE
Found the following hidden files and directories:
.bumpversion.cfg
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
‘inst/doc/decoupleR.html’
‘inst/doc/pw_bk.html’
‘inst/doc/pw_sc.html’
‘inst/doc/tf_bk.html’
‘inst/doc/tf_sc.html’
* 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 R 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 ... WARNING
[2024-03-03 20:05:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 20:05:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:01] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-03 20:05:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 20:05:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:05:02] [TRACE] [OmnipathR] Cache locked: FALSE
'::' or ':::' import not declared from: ‘reshape2’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ulm_analysis: no visible global function definition for ‘cor’
.ulm_analysis: no visible global function definition for ‘pt’
Undefined global functions or variables:
cor pt
Consider adding
importFrom("stats", "cor", "pt")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘decoupleR.Rmd’ ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_dorothea 406.026 5.784 423.823
get_collectri 102.901 1.806 111.815
run_fgsea 21.683 0.336 22.195
run_aucell 8.637 1.114 9.906
get_progeny 6.593 0.569 14.439
* 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:
4. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
5. ├─dplyr::bind_rows(.)
6. │ └─rlang::list2(...)
7. ├─purrr::map(...)
8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
9. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
10. ├─dplyr::group_split(.)
11. ├─dplyr::group_by(., pathway)
12. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
13. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
14. └─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
‘decoupleR.Rmd’
‘pw_bk.Rmd’
‘pw_sc.Rmd’
‘tf_bk.Rmd’
‘tf_sc.Rmd’
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-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/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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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[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 20:16:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:33] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-03-03 20:16:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:35] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-03-03 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:35] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-03-03 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:35] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-03-03 20:16:35] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-03-03 20:16:35] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-03-03 20:16:35] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-03-03 20:16:36] [TRACE] [OmnipathR] HTTP 200
[2024-03-03 20:16:36] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:36] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-03 20:16:36] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-03 20:16:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-03-03 20:16:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-03-03 20:16:38] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-03 20:16:38] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-03-03 20:16:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:38] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-03-03 20:16:38] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:39] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-03 20:16:39] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-03-03 20:16:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:39] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-03-03 20:16:39] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-03-03 20:16:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:49] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:16:49] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-03 20:16:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-03 20:16:52] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-03-03 20:16:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:16:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:52] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-03-03 20:16:52] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-03-03 20:16:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:16:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:16:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:59] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-03 20:16:59] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-03 20:16:59] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-03-03 20:17:01] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)`.
[2024-03-03 20:17:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-03-03 20:17:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:17:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:17:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:17:10] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:17:10] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-03 20:17:13] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-03 20:17:13] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-03-03 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:17:13] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-03-03 20:17:13] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:17:37] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-03 20:17:59] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-03 20:23:46] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-03-03 20:23:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:23:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:24:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-03 20:24:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:24:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:24:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:24:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:24:02] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:24:02] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-03 20:24:04] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-03 20:24:04] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-03-03 20:24:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:24:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:24:04] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-03-03 20:24:04] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:24:14] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-03 20:24:30] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-03 20:28:10] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-03-03 20:28:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:28:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:28:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:28:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:28:23] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:28:23] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-03 20:28:24] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-03 20:28:24] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-03-03 20:28:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:28:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:28:24] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-03-03 20:28:24] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:28:28] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-03 20:28:33] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-03 20:29:52] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-03 20:29:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:29:52] [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`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [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`
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:29:53] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-03 20:29:53] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 20:29:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:29:53] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-03 20:29:53] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-03-03 20:29:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:29:54] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-03 20:29:54] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-03 20:29:54] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:29:58] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-03 20:30:03] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-03 20:31:23] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-03 20:31:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-03 20:31:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 20:31:24] [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`
[2024-03-03 20:31:24] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-03 20:31:24] [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`
[2024-03-03 20:31:24] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-03 20:31:24] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-03 20:31:24] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-03 20:31:25] [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 4 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
Error in `UseMethod("distinct")`: no applicable method for 'distinct' applied to an object of class "NULL"
Backtrace:
▆
1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
2. │ └─... %>% ...
3. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
4. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
5. ├─dplyr::bind_rows(.)
6. │ └─rlang::list2(...)
7. ├─purrr::map(...)
8. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
9. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
10. ├─dplyr::group_split(.)
11. ├─dplyr::group_by(., pathway)
12. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
13. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
14. └─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.103 | 0.013 | 0.116 | |
| convert_f_defaults | 0.030 | 0.003 | 0.034 | |
| decouple | 0.001 | 0.000 | 0.002 | |
| dot-fit_preprocessing | 0.025 | 0.004 | 0.031 | |
| extract_sets | 0.051 | 0.003 | 0.055 | |
| filt_minsize | 0.044 | 0.001 | 0.045 | |
| get_collectri | 102.901 | 1.806 | 111.815 | |
| get_dorothea | 406.026 | 5.784 | 423.823 | |
| get_profile_of | 0.000 | 0.001 | 0.001 | |
| get_progeny | 6.593 | 0.569 | 14.439 | |
| get_resource | 0.420 | 0.040 | 2.054 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.029 | 0.002 | 0.033 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0.001 | 0.000 | 0.001 | |
| randomize_matrix | 0.000 | 0.001 | 0.001 | |
| rename_net | 0.047 | 0.001 | 0.048 | |
| run_aucell | 8.637 | 1.114 | 9.906 | |
| run_consensus | 2.014 | 0.025 | 2.053 | |
| run_fgsea | 21.683 | 0.336 | 22.195 | |
| run_gsva | 1.529 | 0.147 | 1.700 | |
| run_mdt | 0.281 | 0.025 | 0.319 | |
| run_mlm | 0.106 | 0.003 | 0.110 | |
| run_ora | 0.558 | 0.010 | 0.571 | |
| run_udt | 0.419 | 0.018 | 0.446 | |
| run_ulm | 0.069 | 0.002 | 0.071 | |
| run_viper | 0.779 | 0.118 | 0.912 | |
| run_wmean | 0.819 | 0.008 | 0.836 | |
| run_wsum | 0.855 | 0.012 | 0.874 | |
| show_methods | 0.061 | 0.008 | 0.071 | |
| show_resources | 0.062 | 0.006 | 0.600 | |
| tidyeval | 0 | 0 | 0 | |