Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:09 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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: 2024-04-17 11:14:22 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 11:42:42 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 1700.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: decoupleR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.8.2.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 [2024-04-17 11:14:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:55] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Contains 8 files. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-04-17 11:14:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-17 11:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-17 11:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-17 11:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-17 11:14:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:14:56] [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 340.136 2.037 344.120 get_collectri 84.795 0.859 166.339 run_fgsea 26.629 0.132 26.787 run_aucell 10.401 1.081 11.507 get_progeny 8.087 0.365 9.395 * 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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Contains 8 files. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Cache locked: FALSE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:25:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:25:56] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-04-17 11:25:56] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-04-17 11:25:56] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-04-17 11:25:56] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-04-17 11:27:27] [WARN] [OmnipathR] HTTP 504 [2024-04-17 11:27:27] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 [2024-04-17 11:27:32] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-04-17 11:29:02] [WARN] [OmnipathR] HTTP 504 [2024-04-17 11:29:02] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 [2024-04-17 11:29:07] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-04-17 11:29:14] [TRACE] [OmnipathR] HTTP 200 [2024-04-17 11:29:14] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-04-17 11:29:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:14] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-04-17 11:29:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-04-17 11:29:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-04-17 11:29:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-04-17 11:29:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-04-17 11:29:14] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-04-17 11:29:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-04-17 11:29:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-04-17 11:29:14] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-04-17 11:29:14] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-04-17 11:29:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-04-17 11:29:14] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2024-04-17 11:29:15] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-04-17 11:29:15] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-04-17 11:29:15] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2024-04-17 11:29:15] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:29:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:18] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-04-17 11:29:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-04-17 11:29:22] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-04-17 11:29:22] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-04-17 11:29:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:22] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-04-17 11:29:22] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2024-04-17 11:29:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:29:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:29:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:30] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-04-17 11:29:30] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-04-17 11:29:30] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2024-04-17 11:29:31] [TRACE] [OmnipathR] Bypassing call: `OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)`. [2024-04-17 11:29:31] [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. [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:31] [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` [2024-04-17 11:29:39] [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` [2024-04-17 11:29:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:39] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`. [2024-04-17 11:29:39] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-04-17 11:29:43] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-04-17 11:29:43] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1] [2024-04-17 11:29:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:29:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:29:43] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`. [2024-04-17 11:29:43] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:30:06] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-04-17 11:30:25] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any [2024-04-17 11:35:05] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:13] [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` [2024-04-17 11:35:16] [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` [2024-04-17 11:35:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:35:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:35:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:35:16] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`. [2024-04-17 11:35:16] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-04-17 11:35:18] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-04-17 11:35:18] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1] [2024-04-17 11:35:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:35:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:35:18] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`. [2024-04-17 11:35:18] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:35:27] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-04-17 11:35:43] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any [2024-04-17 11:38:52] [SUCCESS] [OmnipathR] Downloaded 234298 interactions. [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:00] [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` [2024-04-17 11:39:03] [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` [2024-04-17 11:39:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:39:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:39:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:39:03] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-04-17 11:39:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-04-17 11:39:05] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-04-17 11:39:05] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-04-17 11:39:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:39:05] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-04-17 11:39:05] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:39:08] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-04-17 11:39:12] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any [2024-04-17 11:40:21] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-04-17 11:40:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:40:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [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` [2024-04-17 11:40:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:40:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:40:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:40:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:40:22] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2024-04-17 11:40:22] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-04-17 11:40:22] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-04-17 11:40:22] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2024-04-17 11:40:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-17 11:40:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:40:22] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2024-04-17 11:40:22] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:40:22] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-04-17 11:40:22] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI [2024-04-17 11:40:22] [SUCCESS] [OmnipathR] Downloaded 232 interactions. [2024-04-17 11:40:22] [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` [2024-04-17 11:40:23] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-04-17 11:40:23] [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` [2024-04-17 11:40:23] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:40:27] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-04-17 11:40:31] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any [2024-04-17 11:41:50] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-04-17 11:41:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-04-17 11:41:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-17 11:41:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-04-17 11:41:50] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-04-17 11:41:50] [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` [2024-04-17 11:41:50] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-04-17 11:41:51] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-04-17 11:41:51] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI [2024-04-17 11:41:51] [SUCCESS] [OmnipathR] Downloaded 232 interactions. | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% 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 | 0.011 | 0.130 | |
convert_f_defaults | 0.030 | 0.003 | 0.033 | |
decouple | 0.002 | 0.001 | 0.002 | |
dot-fit_preprocessing | 0.029 | 0.005 | 0.035 | |
extract_sets | 0.051 | 0.006 | 0.056 | |
filt_minsize | 0.041 | 0.002 | 0.042 | |
get_collectri | 84.795 | 0.859 | 166.339 | |
get_dorothea | 340.136 | 2.037 | 344.120 | |
get_profile_of | 0.000 | 0.001 | 0.000 | |
get_progeny | 8.087 | 0.365 | 9.395 | |
get_resource | 0.387 | 0.037 | 0.992 | |
get_toy_data | 0.003 | 0.000 | 0.003 | |
intersect_regulons | 0.025 | 0.001 | 0.027 | |
pipe | 0 | 0 | 0 | |
pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.039 | 0.001 | 0.040 | |
run_aucell | 10.401 | 1.081 | 11.507 | |
run_consensus | 1.617 | 0.011 | 1.636 | |
run_fgsea | 26.629 | 0.132 | 26.787 | |
run_gsva | 1.373 | 0.088 | 1.463 | |
run_mdt | 0.244 | 0.032 | 0.274 | |
run_mlm | 0.086 | 0.006 | 0.092 | |
run_ora | 0.480 | 0.033 | 0.514 | |
run_udt | 0.333 | 0.009 | 0.343 | |
run_ulm | 0.051 | 0.001 | 0.053 | |
run_viper | 0.758 | 0.065 | 0.826 | |
run_wmean | 0.654 | 0.004 | 0.660 | |
run_wsum | 0.748 | 0.007 | 0.756 | |
show_methods | 0.045 | 0.002 | 0.047 | |
show_resources | 0.059 | 0.004 | 0.117 | |
tidyeval | 0 | 0 | 0 | |