Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-04 11:40:26 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4479 |
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 527/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.10.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: decoupleR |
Version: 2.10.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings decoupleR_2.10.0.tar.gz |
StartedAt: 2024-05-04 06:42:06 -0000 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 07:22:06 -0000 (Sat, 04 May 2024) |
EllapsedTime: 2400.1 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: decoupleR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings decoupleR_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.10.0’ * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE [2024-05-04 06:42:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 06:42:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Contains 8 files. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 06:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-04 06:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-04 06:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-04 06:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-04 06:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-04 06:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 06:42:51] [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 688.238 11.938 708.276 get_collectri 173.831 2.530 183.857 run_fgsea 25.268 0.671 26.004 get_progeny 8.669 0.814 17.835 run_aucell 8.844 0.634 9.500 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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% [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Contains 8 files. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-04 07:00:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:35] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-04 07:00:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:00:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:00:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:37] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-04 07:00:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:37] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-04 07:00:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:37] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-04 07:00:37] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-04 07:00:37] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-04 07:00:37] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-04 07:00:40] [TRACE] [OmnipathR] HTTP 200 [2024-05-04 07:00:40] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2024-05-04 07:00:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:40] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2024-05-04 07:00:40] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2024-05-04 07:00:40] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2024-05-04 07:00:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2024-05-04 07:00:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:41] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2024-05-04 07:00:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-04 07:00:41] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2024-05-04 07:00:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2024-05-04 07:00:43] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2024-05-04 07:00:43] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2024-05-04 07:00:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2024-05-04 07:00:43] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2024-05-04 07:00:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:00:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2024-05-04 07:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:45] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2024-05-04 07:00:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-04 07:00:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2024-05-04 07:00:45] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2024-05-04 07:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:45] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2024-05-04 07:00:45] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2024-05-04 07:00:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:00:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:00:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:00:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:56] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2024-05-04 07:00:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-04 07:00:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-04 07:00:59] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2024-05-04 07:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:00:59] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2024-05-04 07:00:59] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2024-05-04 07:01:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:01:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:01:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-04 07:01:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:01:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:01:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2024-05-04 07:01:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2024-05-04 07:01:06] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2024-05-04 07:01:09] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`. [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:09] [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` [2024-05-04 07:01:19] [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` [2024-05-04 07:01:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:01:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:01:19] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`. [2024-05-04 07:01:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-04 07:01:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`. [2024-05-04 07:01:21] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1] [2024-05-04 07:01:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:01:21] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`. [2024-05-04 07:01:22] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-04 07:01:46] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-04 07:02:17] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-04 07:12:45] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:12:59] [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` [2024-05-04 07:13:04] [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` [2024-05-04 07:13:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:13:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:13:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:13:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:13:04] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`. [2024-05-04 07:13:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-04 07:13:06] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`. [2024-05-04 07:13:06] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1] [2024-05-04 07:13:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:13:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:13:06] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`. [2024-05-04 07:13:06] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-04 07:13:18] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any [2024-05-04 07:13:38] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any; excluding resources: none [2024-05-04 07:21:12] [SUCCESS] [OmnipathR] Downloaded 5294 interactions. [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:12] [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` [2024-05-04 07:21:15] [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` [2024-05-04 07:21:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:21:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:21:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:21:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:21:15] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`. [2024-05-04 07:21:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-04 07:21:16] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`. [2024-05-04 07:21:16] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1] [2024-05-04 07:21:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 07:21:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 07:21:16] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`. [2024-05-04 07:21:16] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-04 07:21:22] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2024-05-04 07:21:28] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any; excluding resources: none
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.091 | 0.016 | 0.108 | |
convert_f_defaults | 0.024 | 0.012 | 0.036 | |
decouple | 0.001 | 0.000 | 0.001 | |
dot-fit_preprocessing | 0.027 | 0.000 | 0.029 | |
extract_sets | 0.028 | 0.000 | 0.028 | |
filt_minsize | 0.050 | 0.004 | 0.054 | |
get_collectri | 173.831 | 2.530 | 183.857 | |
get_dorothea | 688.238 | 11.938 | 708.276 | |
get_profile_of | 0 | 0 | 0 | |
get_progeny | 8.669 | 0.814 | 17.835 | |
get_resource | 0.418 | 0.024 | 3.609 | |
get_toy_data | 0.003 | 0.000 | 0.003 | |
intersect_regulons | 0.031 | 0.000 | 0.031 | |
pipe | 0.001 | 0.000 | 0.000 | |
pivot_wider_profile | 0 | 0 | 0 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.047 | 0.000 | 0.047 | |
run_aucell | 8.844 | 0.634 | 9.500 | |
run_consensus | 2.607 | 0.080 | 2.694 | |
run_fgsea | 25.268 | 0.671 | 26.004 | |
run_gsva | 1.736 | 0.047 | 1.791 | |
run_mdt | 0.170 | 0.026 | 0.189 | |
run_mlm | 0.105 | 0.016 | 0.121 | |
run_ora | 0.618 | 0.016 | 0.635 | |
run_udt | 0.379 | 0.016 | 0.396 | |
run_ulm | 0.082 | 0.012 | 0.094 | |
run_viper | 0.819 | 0.052 | 0.873 | |
run_wmean | 1.070 | 0.052 | 1.124 | |
run_wsum | 0.982 | 0.012 | 0.996 | |
show_methods | 0.071 | 0.000 | 0.072 | |
show_resources | 0.081 | 0.012 | 1.342 | |
tidyeval | 0.000 | 0.000 | 0.001 | |