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 11:36:55 -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 1467/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.12.0 (landing page) Denes Turei
| 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 | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.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. |
Package: OmnipathR |
Version: 3.12.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.tar.gz |
StartedAt: 2024-05-04 01:47:28 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 02:21:34 -0400 (Sat, 04 May 2024) |
EllapsedTime: 2046.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.12.0’ * 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 ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... NOTE [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Contains 1 files. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-04 01:47:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:48] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Contains 1 files. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-04 01:47:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 01:47:58] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘oma_pairwise_translated’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: omnipath_cache_load > ### Title: Loads an R object from the cache > ### Aliases: omnipath_cache_load > > ### ** Examples > > url <- paste0( + 'https://omnipathdb.org/intercell?resources=Adhesome,Almen2009,', + 'Baccin2019,CSPA,CellChatDB&license=academic' + ) > result <- read.delim(url, sep = '\t') > omnipath_cache_save(result, url = url) [2024-05-04 02:08:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 02:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 02:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:07] [INFO] [OmnipathR] Cache item `31d0d863d41fbc3d10dd489849f900bd2ee741c9` version 1: status changed from `unknown` to `started`. [2024-05-04 02:08:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`. [2024-05-04 02:08:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`. [2024-05-04 02:08:07] [INFO] [OmnipathR] Download ready [key=31d0d863d41fbc3d10dd489849f900bd2ee741c9, version=1] [2024-05-04 02:08:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 02:08:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:07] [INFO] [OmnipathR] Cache item `31d0d863d41fbc3d10dd489849f900bd2ee741c9` version 1: status changed from `started` to `ready`. > # works only if you have already this item in the cache > intercell_data <- omnipath_cache_load(url = url) [2024-05-04 02:08:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`. > class(intercell_data) [1] "data.frame" > # [1] "data.frame" > nrow(intercell_data) [1] 17377 > # [1] 16622 > attr(intercell_data, 'origin') [1] "cache" > # [1] "cache" > > # basic example of saving and loading to and from the cache: > bioc_url <- 'https://bioconductor.org/' > bioc_html <- readChar(url(bioc_url), nchars = 99999) Warning in readChar(url(bioc_url), nchars = 99999) : URL 'https://bioconductor.org/': status was 'SSL connect error' Error in readChar(url(bioc_url), nchars = 99999) : cannot open the connection to 'https://bioconductor.org/' Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** 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 [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Contains 8 files. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-03 15:27:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:32] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Contains 1 files. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-03 15:27:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-03 15:27:34] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.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: x86_64-pc-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. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2024 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://r.omnipathdb.org/ > # Git repo: https://github.com/saezlab/OmnipathR > # > > > library(testthat) > library(OmnipathR) [2024-05-04 02:08:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 02:08:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:31] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Contains 2 files. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-04 02:08:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-04 02:08:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-04 02:08:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-04 02:08:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-04 02:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-04 02:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-04 02:08:32] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 22.842 1.836 78.644
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.016 | 0.004 | 0.020 | |
all_uniprots | 0.007 | 0.004 | 0.011 | |
ancestors | 0.006 | 0.003 | 0.010 | |
annotated_network | 1.845 | 0.153 | 54.161 | |
annotation_categories | 98.567 | 0.091 | 100.364 | |
biomart_query | 1.100 | 0.048 | 5.054 | |
bioplex1 | 0.021 | 0.000 | 0.021 | |
bioplex2 | 0.023 | 0.000 | 0.023 | |
bioplex3 | 0.022 | 0.000 | 0.022 | |
bioplex_all | 0.023 | 0.000 | 0.023 | |
bioplex_hct116_1 | 0.024 | 0.000 | 0.023 | |
bma_motif_es | 0.772 | 0.028 | 2.101 | |
bma_motif_vs | 0.351 | 0.012 | 1.180 | |
collectri | 149.237 | 3.405 | 169.359 | |
common_name | 0.029 | 0.000 | 0.029 | |
consensuspathdb_download | 0.001 | 0.000 | 0.001 | |
consensuspathdb_raw_table | 0.013 | 0.004 | 0.016 | |
curated_ligand_receptor_interactions | 5.376 | 0.679 | 17.879 | |
curated_ligrec_stats | 46.590 | 4.127 | 136.529 | |
database_summary | 1.347 | 0.084 | 3.915 | |
descendants | 0.013 | 0.000 | 0.013 | |
dorothea | 78.606 | 0.949 | 87.519 | |
ensembl_dataset | 0.017 | 0.000 | 0.017 | |
ensembl_id_mapping_table | 1.446 | 0.049 | 12.715 | |
ensembl_id_type | 0.004 | 0.000 | 0.004 | |
ensembl_name | 0.080 | 0.004 | 0.084 | |
ensembl_organisms | 0.206 | 0.000 | 0.206 | |
ensembl_organisms_raw | 0.204 | 0.000 | 0.204 | |
ensembl_orthology | 0.000 | 0.000 | 0.001 | |
enzsub_graph | 2.751 | 0.072 | 6.878 | |
evex_download | 0.017 | 0.004 | 0.022 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 23.276 | 0.373 | 39.570 | |
extra_attrs | 4.480 | 0.003 | 4.505 | |
extra_attrs_to_cols | 9.053 | 0.068 | 10.426 | |
filter_by_resource | 5.550 | 7.412 | 26.381 | |
filter_extra_attrs | 34.590 | 2.776 | 55.009 | |
filter_intercell | 8.912 | 7.071 | 36.795 | |
filter_intercell_network | 0.048 | 0.004 | 0.097 | |
find_all_paths | 9.775 | 0.269 | 25.267 | |
from_evidences | 0.001 | 0.000 | 0.001 | |
get_annotation_resources | 0.229 | 0.000 | 1.157 | |
get_complex_genes | 2.241 | 0.259 | 6.226 | |
get_complex_resources | 0.250 | 0.028 | 1.120 | |
get_db | 0.000 | 0.000 | 0.001 | |
get_enzsub_resources | 0.241 | 0.032 | 1.055 | |
get_interaction_resources | 0.449 | 0.060 | 1.237 | |
get_intercell_categories | 0.673 | 0.052 | 1.203 | |
get_intercell_generic_categories | 0.198 | 0.011 | 0.209 | |
get_intercell_resources | 0.224 | 0.012 | 0.933 | |
get_ontology_db | 0.045 | 0.000 | 0.045 | |
get_resources | 0.240 | 0.028 | 0.948 | |
get_signed_ptms | 6.867 | 0.260 | 9.815 | |
giant_component | 9.691 | 0.568 | 13.152 | |
go_annot_download | 16.043 | 1.077 | 27.092 | |
go_annot_slim | 0.000 | 0.000 | 0.001 | |
go_ontology_download | 0.023 | 0.001 | 0.035 | |
guide2pharma_download | 0.021 | 0.000 | 0.020 | |
harmonizome_download | 0.023 | 0.000 | 0.038 | |
has_extra_attrs | 10.323 | 0.082 | 10.932 | |
homologene_download | 0.022 | 0.000 | 0.023 | |
homologene_raw | 0.136 | 0.000 | 0.136 | |
homologene_uniprot_orthology | 0.026 | 0.016 | 0.041 | |
hpo_download | 3.341 | 0.453 | 4.674 | |
htridb_download | 0.029 | 0.000 | 0.029 | |
import_all_interactions | 3.886 | 0.274 | 7.864 | |
import_intercell_network | 0.022 | 0.000 | 0.022 | |
import_kinaseextra_interactions | 2.455 | 0.193 | 5.003 | |
import_ligrecextra_interactions | 1.272 | 0.047 | 3.322 | |
import_lncrna_mrna_interactions | 0.904 | 0.036 | 2.157 | |
import_mirnatarget_interactions | 1.721 | 0.090 | 4.149 | |
import_omnipath_annotations | 1.042 | 0.015 | 2.521 | |
import_omnipath_complexes | 1.158 | 0.064 | 3.469 | |
import_omnipath_enzsub | 2.087 | 0.068 | 4.160 | |
import_omnipath_interactions | 0.527 | 0.015 | 1.481 | |
import_omnipath_intercell | 1.112 | 0.062 | 2.729 | |
import_pathwayextra_interactions | 1.551 | 0.134 | 6.564 | |
import_post_translational_interactions | 1.756 | 0.157 | 5.074 | |
import_small_molecule_protein_interactions | 1.043 | 0.040 | 2.267 | |
import_tf_mirna_interactions | 1.421 | 0.198 | 3.800 | |
import_tf_target_interactions | 2.713 | 0.247 | 6.060 | |
import_transcriptional_interactions | 4.297 | 0.299 | 8.112 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.047 | 0.000 | 0.055 | |
interaction_graph | 0.472 | 0.032 | 1.268 | |
interaction_types | 0.031 | 0.004 | 0.036 | |
intercell_categories | 0.046 | 0.012 | 0.058 | |
intercell_consensus_filter | 1.255 | 1.237 | 9.501 | |
is_ontology_id | 0.000 | 0.000 | 0.001 | |
is_swissprot | 0.046 | 0.016 | 0.081 | |
is_trembl | 0.030 | 0.008 | 0.037 | |
is_uniprot | 0.010 | 0.003 | 0.013 | |
kegg_info | 0.014 | 0.004 | 0.018 | |
kegg_open | 0.014 | 0.004 | 0.019 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.015 | 0.004 | 0.019 | |
kegg_pathway_list | 0.013 | 0.004 | 0.018 | |
kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
kegg_picture | 0.224 | 0.039 | 4.955 | |
kegg_process | 0.045 | 0.008 | 0.078 | |
latin_name | 0.072 | 0.015 | 0.164 | |
load_db | 0.268 | 0.041 | 0.835 | |
ncbi_taxid | 0.092 | 0.000 | 0.117 | |
nichenet_build_model | 0.001 | 0.000 | 0.000 | |
nichenet_expression_data | 0.025 | 0.001 | 0.071 | |
nichenet_gr_network | 0.063 | 0.006 | 0.129 | |
nichenet_gr_network_evex | 0.020 | 0.004 | 0.056 | |
nichenet_gr_network_harmonizome | 0.025 | 0.000 | 0.053 | |
nichenet_gr_network_htridb | 0.026 | 0.000 | 0.042 | |
nichenet_gr_network_omnipath | 20.720 | 13.329 | 129.006 | |
nichenet_gr_network_pathwaycommons | 0.029 | 0.097 | 0.196 | |
nichenet_gr_network_regnetwork | 0.007 | 0.008 | 0.016 | |
nichenet_gr_network_remap | 0.012 | 0.004 | 0.016 | |
nichenet_gr_network_trrust | 0.017 | 0.008 | 0.028 | |
nichenet_ligand_activities | 0.001 | 0.000 | 0.000 | |
nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
nichenet_ligand_target_matrix | 0.000 | 0.000 | 0.001 | |
nichenet_lr_network | 0.035 | 0.009 | 0.050 | |
nichenet_lr_network_guide2pharma | 0.015 | 0.000 | 0.015 | |
nichenet_lr_network_omnipath | 0.029 | 0.012 | 0.042 | |
nichenet_lr_network_ramilowski | 0.011 | 0.004 | 0.025 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.063 | 0.179 | 0.496 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.037 | 0.103 | 0.279 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.031 | 0.012 | 0.044 | |
nichenet_signaling_network_cpdb | 0.007 | 0.004 | 0.011 | |
nichenet_signaling_network_evex | 0.055 | 0.029 | 0.084 | |
nichenet_signaling_network_harmonizome | 0.016 | 0.004 | 0.020 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 8.229 | 49.886 | 73.193 | |
nichenet_signaling_network_pathwaycommons | 0.008 | 0.007 | 0.018 | |
nichenet_signaling_network_vinayagam | 0.011 | 0.004 | 0.015 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0.001 | 0.000 | 0.000 | |
obo_parser | 0.091 | 1.540 | 3.753 | |
oma_code | 0.022 | 0.004 | 0.031 | |
oma_organisms | 0.062 | 0.000 | 0.088 | |
oma_pairwise | 0.014 | 0.000 | 0.014 | |
oma_pairwise_genesymbols | 0.009 | 0.004 | 0.017 | |
omnipath | 4.360 | 3.936 | 10.466 | |
omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
omnipath_cache_clean | 0.008 | 0.002 | 0.012 | |
omnipath_cache_clean_db | 0.082 | 0.028 | 0.113 | |
omnipath_cache_download_ready | 0.503 | 0.089 | 1.245 | |
omnipath_cache_filter_versions | 0.091 | 0.005 | 0.102 | |
omnipath_cache_get | 0.123 | 0.004 | 0.129 | |
omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
omnipath_cache_latest_or_new | 0.059 | 0.000 | 0.059 | |