Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-09 11:40:45 -0400 (Thu, 09 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
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 | ERROR | skipped | skipped | |||||||||
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: 2024-05-09 06:35:27 -0000 (Thu, 09 May 2024) |
EndedAt: 2024-05-09 07:15:27 -0000 (Thu, 09 May 2024) |
EllapsedTime: 2400.2 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 [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Contains 8 files. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-09 06:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:11] [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 ... ERROR Running examples in ‘decoupleR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_collectri > ### Title: CollecTRI gene regulatory network. Wrapper to access CollecTRI > ### gene regulatory network. CollecTRI is a comprehensive resource > ### containing a curated collection of transcription factors (TFs) and > ### their target genes. It is an expansion of DoRothEA. Each interaction > ### is weighted by its mode of regulation (either positive or negative). > ### Aliases: get_collectri > > ### ** Examples > > collectri <- get_collectri(organism='human', split_complexes=FALSE) [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Contains 1 files. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-09 06:36:46] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:36:46] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-09 06:36:46] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-09 06:36:46] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:36:46] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:39:49] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:39:49] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2024-05-09 06:39:54] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:43:00] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:43:00] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2024-05-09 06:43:05] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:46:08] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:46:08] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2024-05-09 06:46:08] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-09 06:46:08] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-09 06:46:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:46:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:46:08] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-05-09 06:46:08] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-05-09 06:46:08] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:46:08] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:49:15] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:49:15] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2024-05-09 06:49:20] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:52:23] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:52:23] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2024-05-09 06:52:28] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:55:31] [WARN] [OmnipathR] HTTP 404 [2024-05-09 06:55:31] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2024-05-09 06:55:31] [WARN] [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2024-05-09 06:55:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:31] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:31] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:31] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:35] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2024-05-09 06:55:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:55:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:55:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:55:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:55:35] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2024-05-09 06:55:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-05-09 06:55:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2024-05-09 06:55:35] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2024-05-09 06:55:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:55:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:55:35] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2024-05-09 06:55:35] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2024-05-09 06:55:42] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Error in if (.keep) . else select(., -!!evs_col) : argument is of length zero Calls: get_collectri ... tidyselect_data_has_predicates -> unnest_evidences -> %>% Execution halted * 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% [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Contains 4 files. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-09 06:57:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:00] [TRACE] [OmnipathR] Cache locked: FALSE [2024-05-09 06:57:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-09 06:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2024-05-09 06:57:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-09 06:57:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:57:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:03] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-09 06:57:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 06:57:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 06:57:03] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2024-05-09 06:57:03] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2024-05-09 06:57:03] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-09 06:57:03] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:00:06] [WARN] [OmnipathR] HTTP 404 [2024-05-09 07:00:06] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2024-05-09 07:00:11] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:03:13] [WARN] [OmnipathR] HTTP 404 [2024-05-09 07:03:13] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2024-05-09 07:03:18] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:06:27] [WARN] [OmnipathR] HTTP 404 [2024-05-09 07:06:27] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2024-05-09 07:06:27] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2024-05-09 07:06:27] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2024-05-09 07:06:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-09 07:06:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-09 07:06:27] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2024-05-09 07:06:27] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2024-05-09 07:06:27] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:06:27] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:09:29] [WARN] [OmnipathR] HTTP 404 [2024-05-09 07:09:29] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2024-05-09 07:09:34] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2024-05-09 07:12:39] [WARN] [OmnipathR] HTTP 404 [2024-05-09 07:12:39] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2024-05-09 07:12:44] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.101 | 0.008 | 0.110 | |
convert_f_defaults | 0.037 | 0.000 | 0.037 | |
decouple | 0.001 | 0.000 | 0.001 | |
dot-fit_preprocessing | 0.029 | 0.000 | 0.030 | |
extract_sets | 0.029 | 0.000 | 0.029 | |
filt_minsize | 0.053 | 0.000 | 0.053 | |