Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-24 11:43 -0500 (Fri, 24 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4609 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4393 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3839 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 3835 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
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 517/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decoupleR 2.13.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
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: 2.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.13.0.tar.gz |
StartedAt: 2025-01-24 07:10:15 -0000 (Fri, 24 Jan 2025) |
EndedAt: 2025-01-24 07:50:16 -0000 (Fri, 24 Jan 2025) |
EllapsedTime: 2400.9 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: decoupleR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decoupleR_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.13.0’ * 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 ...Warning: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Contains 4 files. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-24 07:10:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:10:58] [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(s) in Rd file 'run_gsva.Rd': ‘GSVA::gsva’ ‘GeneSetCollection’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: run_gsva.Rd: GSVA::gsva, GeneSetCollection Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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) Warning: program compiled against libxml 212 using older 211 [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Contains 1 files. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [TRACE] [OmnipathR] Cache locked: FALSE [2025-01-24 07:11:36] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:11:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:11:36] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-01-24 07:11:36] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-01-24 07:11:36] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:11:36] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:14:39] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:14:39] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2025-01-24 07:14:44] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:17:46] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:17:46] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2025-01-24 07:17:51] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:20:52] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:20:52] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2025-01-24 07:20:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-01-24 07:20:52] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-01-24 07:20:52] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-01-24 07:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:20:53] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2025-01-24 07:20:53] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2025-01-24 07:20:53] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:20:53] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:23:54] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:23:54] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2025-01-24 07:23:59] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:27:11] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:27:11] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2025-01-24 07:27:16] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:30:21] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:30:21] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2025-01-24 07:30:22] [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. [2025-01-24 07:30:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:22] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:22] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:22] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:25] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-01-24 07:30:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:30:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:30:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:30:25] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2025-01-24 07:30:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-01-24 07:30:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-01-24 07:30:26] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2025-01-24 07:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:30:26] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2025-01-24 07:30:26] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-01-24 07:30:33] [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/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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% Warning: program compiled against libxml 212 using older 211 [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Contains 4 files. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-24 07:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:50] [TRACE] [OmnipathR] Cache locked: FALSE [2025-01-24 07:31:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-01-24 07:31:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-01-24 07:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:53] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-01-24 07:31:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:53] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-01-24 07:31:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:31:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:31:53] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-01-24 07:31:53] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-01-24 07:31:53] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:31:53] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:35:01] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:35:01] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2025-01-24 07:35:06] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:38:31] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:38:31] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2025-01-24 07:38:36] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:41:43] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:41:43] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 404 [2025-01-24 07:41:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations] [2025-01-24 07:41:43] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-01-24 07:41:43] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-01-24 07:41:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-24 07:41:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-24 07:41:44] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2. [2025-01-24 07:41:44] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html [2025-01-24 07:41:44] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:41:44] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:44:46] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:44:46] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 404 [2025-01-24 07:44:51] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html` [2025-01-24 07:47:52] [WARN] [OmnipathR] HTTP 404 [2025-01-24 07:47:52] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 [2025-01-24 07:47:57] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.097 | 0.019 | 0.118 | |
convert_f_defaults | 0.032 | 0.004 | 0.036 | |
decouple | 0.000 | 0.000 | 0.001 | |
dot-fit_preprocessing | 0.032 | 0.000 | 0.033 | |
extract_sets | 0.032 | 0.000 | 0.032 | |
filt_minsize | 0.055 | 0.000 | 0.056 | |