| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:19 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | ERROR | ERROR | ||||||||
|
To the developers/maintainers of the decoupleR package: - 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: 2024-03-27 10:49:36 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 11:13:19 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 1423.1 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-mac-arm64/meat/decoupleR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* 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
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:50:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:09] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-27 10:50:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:50:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:50:10] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2024-03-27 10:50:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 10:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 10:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 10:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 10:50:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:50:10] [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 336.474 1.955 338.900
get_collectri 83.887 0.903 86.429
run_fgsea 31.614 0.137 31.820
run_aucell 10.782 0.601 11.387
get_progeny 7.772 0.384 8.910
* 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:
[97] 0.29 - 0.49 [97]
... ... ... and 4 more ...
`actual$p_value[104:113]`: 0.98 0.20 0.20 0.22 0.22 0.87 0.87 0.19 0.19 0.18
`expected$p_value[104:113]`: 0.98 0.20 0.20 0.21 0.21 0.94 0.94 0.19 0.19 0.18
`actual$p_value[118:127]`: 0.13 0.11 0.11 0.99 0.99 0.12 0.12 0.16 0.16 0.59
`expected$p_value[118:127]`: 0.13 0.11 0.11 1.00 1.00 0.13 0.13 0.16 0.16 0.59
`actual$p_value[132:139]`: 0.12 0.59 0.59 0.17 0.17 0.20 0.20 0.59
`expected$p_value[132:139]`: 0.12 0.59 0.59 0.18 0.18 0.20 0.20 0.59
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 33 ]
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-mac-arm64/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-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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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[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:50] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-03-27 10:59:50] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 10:59:50] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 10:59:51] [TRACE] [OmnipathR] HTTP 200
[2024-03-27 10:59:51] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:51] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 10:59:51] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 10:59:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 10:59:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 10:59:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-03-27 10:59:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-27 10:59:52] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-03-27 10:59:52] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-03-27 10:59:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 10:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 10:59:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 10:59:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:55] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-03-27 10:59:55] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 10:59:59] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 10:59:59] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-03-27 10:59:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 10:59:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 10:59:59] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-03-27 10:59:59] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-03-27 11:00:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 11:00:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:00:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 11:00:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:00:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 11:00:07] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 11:00:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 11:00:07] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-03-27 11:00:09] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)`.
[2024-03-27 11:00:09] [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.
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:09] [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`
[2024-03-27 11:00:17] [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`
[2024-03-27 11:00:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:00:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:00:17] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-03-27 11:00:17] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 11:00:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 11:00:21] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-03-27 11:00:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:00:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:00:21] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-03-27 11:00:21] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:00:44] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-27 11:01:02] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-27 11:05:49] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:05:57] [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`
[2024-03-27 11:06:07] [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`
[2024-03-27 11:06:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:06:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:06:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:06:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:06:07] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-03-27 11:06:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-27 11:06:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-27 11:06:09] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-03-27 11:06:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:06:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:06:09] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-03-27 11:06:09] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:06:18] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-27 11:06:34] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-27 11:09:36] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:44] [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`
[2024-03-27 11:09:46] [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`
[2024-03-27 11:09:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:09:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:09:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:09:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:09:46] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-03-27 11:09:46] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 11:09:47] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 11:09:47] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-03-27 11:09:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:09:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:09:47] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-03-27 11:09:47] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:09:50] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-27 11:09:54] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-27 11:11:03] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 11:11:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [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`
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:11:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:11:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:11:03] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 11:11:03] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 11:11:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:11:03] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 11:11:03] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 11:11:04] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-03-27 11:11:04] [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`
[2024-03-27 11:11:05] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 11:11:05] [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`
[2024-03-27 11:11:05] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:11:08] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-27 11:11:13] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-27 11:12:27] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-27 11:12:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 11:12:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 11:12:27] [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`
[2024-03-27 11:12:27] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 11:12:27] [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`
[2024-03-27 11:12:27] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 11:12:27] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 11:12:27] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 11:12:28] [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 2 | WARN 4 | SKIP 0 | PASS 33 ]
══ 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)
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).
actual vs expected
p_value
actual[1, ] 0.075479709
actual[2, ] 0.075479709
- actual[3, ] 0.511687342
+ expected[3, ] 0.548454870
- actual[4, ] 0.511687342
+ expected[4, ] 0.548454870
actual[5, ] 0.010000000
actual[6, ] 0.010000000
actual[7, ] 0.076411558
actual vs expected
p_value
actual[12, ] 0.010000000
actual[13, ] 0.114238030
actual[14, ] 0.114238030
- actual[15, ] 0.510665738
+ expected[15, ] 0.522337972
- actual[16, ] 0.510665738
+ expected[16, ] 0.522337972
actual[17, ] 0.010000000
actual[18, ] 0.010000000
actual[19, ] 0.004682543
actual[20, ] 0.004682543
- actual[21, ] 0.219233595
+ expected[21, ] 0.294730294
and 10 more ...
actual vs expected
p_value
actual[34, ] 1.000000000
actual[35, ] 0.010000000
actual[36, ] 0.010000000
- actual[37, ] 0.091542106
+ expected[37, ] 0.103646587
- actual[38, ] 0.091542106
+ expected[38, ] 0.103646587
actual[39, ] 0.592371428
actual[40, ] 0.592371428
actual[41, ] 0.010000000
actual vs expected
p_value
actual[52, ] 0.976649086
actual[53, ] 0.010000000
actual[54, ] 0.010000000
- actual[55, ] 0.066624941
+ expected[55, ] 0.076411558
- actual[56, ] 0.066624941
+ expected[56, ] 0.076411558
actual[57, ] 0.592371428
actual[58, ] 0.592371428
actual[59, ] 0.010000000
actual[60, ] 0.010000000
- actual[61, ] 0.111211902
+ expected[61, ] 0.108185775
and 4 more ...
actual vs expected
p_value
actual[70, ] 1.000000000
actual[71, ] 0.010000000
actual[72, ] 0.010000000
- actual[73, ] 0.256981914
+ expected[73, ] 0.469812943
- actual[74, ] 0.256981914
+ expected[74, ] 0.469812943
- actual[75, ] 0.133907888
+ expected[75, ] 0.132394821
- actual[76, ] 0.133907888
+ expected[76, ] 0.132394821
actual[77, ] 0.123204721
actual[78, ] 0.123204721
- actual[79, ] 0.146641013
+ expected[79, ] 0.207618744
and 4 more ...
actual vs expected
p_value
actual[88, ] 0.177906190
actual[89, ] 0.154281338
actual[90, ] 0.154281338
- actual[91, ] 0.434796297
+ expected[91, ] 0.487321278
- actual[92, ] 0.434796297
+ expected[92, ] 0.487321278
actual[93, ] 0.009411332
actual[94, ] 0.009411332
actual[95, ] 0.005020222
actual[96, ] 0.005020222
- actual[97, ] 0.294730294
+ expected[97, ] 0.493157392
and 16 more ...
actual vs expected
p_value
actual[118, ] 0.126342554
actual[119, ] 0.111593916
actual[120, ] 0.111593916
- actual[121, ] 0.991185346
+ expected[121, ] 1.000000000
- actual[122, ] 0.991185346
+ expected[122, ] 1.000000000
- actual[123, ] 0.123316421
+ expected[123, ] 0.126342554
- actual[124, ] 0.123316421
+ expected[124, ] 0.126342554
actual[125, ] 0.155922629
actual[126, ] 0.155922629
actual[127, ] 0.592371428
actual vs expected
p_value
actual[132, ] 0.124515409
actual[133, ] 0.592371428
actual[134, ] 0.592371428
- actual[135, ] 0.174865133
+ expected[135, ] 0.183988307
- actual[136, ] 0.174865133
+ expected[136, ] 0.183988307
actual[137, ] 0.198360798
actual[138, ] 0.198360798
actual[139, ] 0.592371428
`actual$p_value[1:7]`: 0.08 0.08 0.51 0.51 0.01 0.01 0.08
`expected$p_value[1:7]`: 0.08 0.08 0.55 0.55 0.01 0.01 0.08
actual$p_value | expected$p_value
[12] 0.01 | 0.01 [12]
[13] 0.11 | 0.11 [13]
[14] 0.11 | 0.11 [14]
[15] 0.51 - 0.52 [15]
[16] 0.51 - 0.52 [16]
[17] 0.01 | 0.01 [17]
[18] 0.01 | 0.01 [18]
[19] 0.00 | 0.00 [19]
[20] 0.00 | 0.00 [20]
[21] 0.22 - 0.29 [21]
... ... ... and 10 more ...
`actual$p_value[34:41]`: 1.00 0.01 0.01 0.09 0.09 0.59 0.59 0.01
`expected$p_value[34:41]`: 1.00 0.01 0.01 0.10 0.10 0.59 0.59 0.01
`actual$p_value[52:59]`: 0.98 0.01 0.01 0.07 0.07 0.59 0.59 0.01
`expected$p_value[52:59]`: 0.98 0.01 0.01 0.08 0.08 0.59 0.59 0.01
actual$p_value | expected$p_value
[70] 1.00 | 1.00 [70]
[71] 0.01 | 0.01 [71]
[72] 0.01 | 0.01 [72]
[73] 0.26 - 0.47 [73]
[74] 0.26 - 0.47 [74]
[75] 0.13 | 0.13 [75]
[76] 0.13 | 0.13 [76]
[77] 0.12 | 0.12 [77]
[78] 0.12 | 0.12 [78]
[79] 0.15 - 0.21 [79]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[88] 0.18 | 0.18 [88]
[89] 0.15 | 0.15 [89]
[90] 0.15 | 0.15 [90]
[91] 0.43 - 0.49 [91]
[92] 0.43 - 0.49 [92]
[93] 0.01 | 0.01 [93]
[94] 0.01 | 0.01 [94]
[95] 0.01 | 0.01 [95]
[96] 0.01 | 0.01 [96]
[97] 0.29 - 0.49 [97]
... ... ... and 4 more ...
`actual$p_value[104:113]`: 0.98 0.20 0.20 0.22 0.22 0.87 0.87 0.19 0.19 0.18
`expected$p_value[104:113]`: 0.98 0.20 0.20 0.21 0.21 0.94 0.94 0.19 0.19 0.18
`actual$p_value[118:127]`: 0.13 0.11 0.11 0.99 0.99 0.12 0.12 0.16 0.16 0.59
`expected$p_value[118:127]`: 0.13 0.11 0.11 1.00 1.00 0.13 0.13 0.16 0.16 0.59
`actual$p_value[132:139]`: 0.12 0.59 0.59 0.17 0.17 0.20 0.20 0.59
`expected$p_value[132:139]`: 0.12 0.59 0.59 0.18 0.18 0.20 0.20 0.59
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.117 | 0.010 | 0.128 | |
| convert_f_defaults | 0.027 | 0.005 | 0.031 | |
| decouple | 0.001 | 0.001 | 0.002 | |
| dot-fit_preprocessing | 0.027 | 0.005 | 0.033 | |
| extract_sets | 0.046 | 0.010 | 0.056 | |
| filt_minsize | 0.039 | 0.002 | 0.041 | |
| get_collectri | 83.887 | 0.903 | 86.429 | |
| get_dorothea | 336.474 | 1.955 | 338.900 | |
| get_profile_of | 0.000 | 0.001 | 0.000 | |
| get_progeny | 7.772 | 0.384 | 8.910 | |
| get_resource | 0.364 | 0.035 | 0.907 | |
| get_toy_data | 0.003 | 0.000 | 0.003 | |
| intersect_regulons | 0.023 | 0.001 | 0.024 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.034 | 0.001 | 0.034 | |
| run_aucell | 10.782 | 0.601 | 11.387 | |
| run_consensus | 1.712 | 0.027 | 1.738 | |
| run_fgsea | 31.614 | 0.137 | 31.820 | |
| run_gsva | 1.341 | 0.085 | 1.426 | |
| run_mdt | 0.235 | 0.027 | 0.260 | |
| run_mlm | 0.089 | 0.003 | 0.092 | |
| run_ora | 0.473 | 0.021 | 0.493 | |
| run_udt | 0.348 | 0.010 | 0.359 | |
| run_ulm | 0.053 | 0.001 | 0.054 | |
| run_viper | 0.755 | 0.061 | 0.819 | |
| run_wmean | 0.646 | 0.004 | 0.651 | |
| run_wsum | 0.723 | 0.007 | 0.729 | |
| show_methods | 0.053 | 0.003 | 0.055 | |
| show_resources | 0.059 | 0.004 | 0.112 | |
| tidyeval | 0.000 | 0.000 | 0.001 | |