Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:02 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 511/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.11.0 (landing page) Pau Badia-i-Mompel
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
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: 2.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.11.0.tar.gz |
StartedAt: 2024-05-12 10:58:51 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 11:29:16 -0400 (Sun, 12 May 2024) |
EllapsedTime: 1825.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: decoupleR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/decoupleR.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘decoupleR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Contains 8 files. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-12 10:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 10:59:31] [TRACE] [OmnipathR] Cache locked: FALSE * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in Rd file 'run_gsva.Rd': ‘GSVA::gsva’ ‘GeneSetCollection’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_dorothea 433.951 3.119 441.631 get_collectri 116.271 1.282 133.367 run_fgsea 29.986 0.251 30.369 run_aucell 11.794 1.038 12.886 get_progeny 7.714 0.388 8.555 * 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 1 | SKIP 0 | PASS 33 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc-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/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(decoupleR) > > test_check("decoupleR") | | | 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% [2024-05-12 11:11:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:49] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 11:11:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-12 11:11:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 11:11:49] [TRACE] [OmnipathR] Contains 8 files. [2024-05-12 11:11:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-12 11:11:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-12 11:11:50] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-12 11:11:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:50] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-12 11:11:50] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-12 11:11:50] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-12 11:11:50] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-12 11:11:51] [TRACE] [OmnipathR] HTTP 200 [2024-05-12 11:11:51] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-05-12 11:11:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:51] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-05-12 11:11:51] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-05-12 11:11:51] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-05-12 11:11:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-05-12 11:11:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-05-12 11:11:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-12 11:11:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-05-12 11:11:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-12 11:11:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-05-12 11:11:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2024-05-12 11:11:52] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-12 11:11:52] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-12 11:11:52] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2024-05-12 11:11:52] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:11:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:55] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-05-12 11:11:55] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-12 11:11:59] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-12 11:11:59] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-05-12 11:11:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:11:59] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-05-12 11:11:59] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2024-05-12 11:12:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:12:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:12:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:12:06] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-12 11:12:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-12 11:12:06] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2024-05-12 11:12:09] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`. [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:09] [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` [2024-05-12 11:12:16] [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` [2024-05-12 11:12:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:12:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:12:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:12:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:12:16] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`. [2024-05-12 11:12:16] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-12 11:12:20] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-12 11:12:20] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1] [2024-05-12 11:12:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:12:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:12:20] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`. [2024-05-12 11:12:20] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:12:41] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-12 11:13:04] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-12 11:19:32] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2024-05-12 11:19:41] [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` [2024-05-12 11:19:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-05-12 11:19:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-05-12 11:19:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` [2024-05-12 11:19:41] [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` [2024-05-12 11:19:41] [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` [2024-05-12 11:19:41] [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` [2024-05-12 11:19:43] [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` [2024-05-12 11:19:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:19:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:19:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:19:44] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`. [2024-05-12 11:19:44] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-12 11:19:46] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-12 11:19:46] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1] [2024-05-12 11:19:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:19:46] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`. [2024-05-12 11:19:46] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:19:59] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-12 11:20:11] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-12 11:24:46] [SUCCESS] [OmnipathR] Downloaded 5294 interactions. [2024-05-12 11:24:46] [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` [2024-05-12 11:24:46] [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` [2024-05-12 11:24:46] [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` [2024-05-12 11:24:46] [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` [2024-05-12 11:24:46] [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` [2024-05-12 11:24:47] [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` [2024-05-12 11:24:47] [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` [2024-05-12 11:24:48] [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` [2024-05-12 11:24:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:24:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:24:48] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-05-12 11:24:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-12 11:24:49] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-12 11:24:49] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-05-12 11:24:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:24:49] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-05-12 11:24:49] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:24:53] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-05-12 11:24:57] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-05-12 11:26:29] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-05-12 11:26:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [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` [2024-05-12 11:26:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:26:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:26:29] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2024-05-12 11:26:29] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-12 11:26:29] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-12 11:26:29] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2024-05-12 11:26:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-12 11:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:26:29] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2024-05-12 11:26:29] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:26:29] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-05-12 11:26:30] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-05-12 11:26:30] [SUCCESS] [OmnipathR] Downloaded 232 interactions. [2024-05-12 11:26:30] [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` [2024-05-12 11:26:31] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-12 11:26:31] [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` [2024-05-12 11:26:31] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:26:35] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-05-12 11:26:39] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none [2024-05-12 11:28:16] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2024-05-12 11:28:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-12 11:28:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-12 11:28:16] [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` [2024-05-12 11:28:16] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2024-05-12 11:28:16] [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` [2024-05-12 11:28:16] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-12 11:28:16] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2024-05-12 11:28:16] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2024-05-12 11:28:17] [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 1 | SKIP 0 | PASS 33 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-omnipath.R:19:3'): test get_progeny mouse ────────────────────── Error in `sym(organism_b)`: Can't convert an integer vector to a symbol. Backtrace: ▆ 1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3 2. │ ├─... %>% ... 3. │ └─decoupleR::get_resource("PROGENy", organism = organism) 4. │ └─... %>% ... 5. ├─rlang::set_names(., c("source", "target", "weight", "p_value")) 6. ├─dplyr::select(., pathway, genesymbol, weight, p_value) 7. ├─dplyr::bind_rows(.) 8. │ └─rlang::list2(...) 9. ├─purrr::map(...) 10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 11. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env) 12. ├─dplyr::group_split(.) 13. ├─dplyr::group_by(., pathway) 14. ├─dplyr::select(., genesymbol, p_value, pathway, weight) 15. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value)) 16. ├─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE) 17. ├─... %>% ... 18. ├─OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism) 19. ├─OmnipathR::orthology_translate_column(...) 20. │ ├─... %>% ... 21. │ └─OmnipathR::get_db(db_name, param = orthology_param) 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) `<fn>`(organism_a = 9606L, organism_b = 10090L) 25. │ └─environment() %>% as.list %>% ... 26. ├─rlang::set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL)) 27. ├─dplyr::select(., -any_of("hgroup")) 28. ├─rlang::exec(oma_pairwise_translated, !!!.) 29. ├─OmnipathR (local) `<fn>`(...) 30. │ └─... %>% ... 31. ├─dplyr::filter(., !is.na(id_organism_a) & !is.na(id_organism_b)) 32. ├─OmnipathR::translate_ids(...) 33. │ ├─... %>% ncbi_taxid 34. │ ├─OmnipathR:::.nse_ensure_str(!!enquo(organism)) 35. │ │ ├─enquo(arg) %>% ... 36. │ │ └─rlang::enquo(arg) 37. │ └─rlang::enquo(organism) 38. ├─OmnipathR::ncbi_taxid(.) 39. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 40. ├─purrr::map_int(., taxon_name, "ncbi") 41. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 42. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env) 43. └─rlang::sym(organism_b) 44. └─rlang:::abort_coercion(x, "a symbol") 45. └─rlang::abort(msg, call = call) ── 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 1 | SKIP 0 | PASS 33 ] Error: Test failures Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.106 | 0.009 | 0.130 | |
convert_f_defaults | 0.030 | 0.003 | 0.036 | |
decouple | 0.001 | 0.001 | 0.002 | |
dot-fit_preprocessing | 0.030 | 0.003 | 0.039 | |
extract_sets | 0.026 | 0.001 | 0.031 | |
filt_minsize | 0.047 | 0.001 | 0.052 | |
get_collectri | 116.271 | 1.282 | 133.367 | |
get_dorothea | 433.951 | 3.119 | 441.631 | |
get_profile_of | 0.000 | 0.001 | 0.000 | |
get_progeny | 7.714 | 0.388 | 8.555 | |
get_resource | 0.384 | 0.032 | 0.560 | |
get_toy_data | 0.003 | 0.000 | 0.004 | |
intersect_regulons | 0.027 | 0.001 | 0.029 | |
pipe | 0 | 0 | 0 | |
pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.040 | 0.001 | 0.042 | |
run_aucell | 11.794 | 1.038 | 12.886 | |
run_consensus | 1.857 | 0.011 | 1.874 | |
run_fgsea | 29.986 | 0.251 | 30.369 | |
run_gsva | 1.550 | 0.124 | 1.680 | |
run_mdt | 0.149 | 0.028 | 0.180 | |
run_mlm | 0.096 | 0.008 | 0.104 | |
run_ora | 0.509 | 0.027 | 0.538 | |
run_udt | 0.284 | 0.019 | 0.305 | |
run_ulm | 0.074 | 0.006 | 0.080 | |
run_viper | 0.812 | 0.124 | 0.954 | |
run_wmean | 0.855 | 0.017 | 0.876 | |
run_wsum | 0.674 | 0.005 | 0.680 | |
show_methods | 0.051 | 0.004 | 0.054 | |
show_resources | 0.060 | 0.005 | 0.112 | |
tidyeval | 0.000 | 0.000 | 0.001 | |