Denes Turei
| Snapshot Date: 2025-01-27 13:40 -0500 (Mon, 27 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: bc4d2dd |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-28 11:46 -0500 (Tue, 28 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" | 4659 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4454 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4465 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4419 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4409 |
| 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 1454/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.15.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
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: 3.15.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.15.0.tar.gz |
| StartedAt: 2025-01-27 20:26:20 -0500 (Mon, 27 Jan 2025) |
| EndedAt: 2025-01-27 20:40:32 -0500 (Mon, 27 Jan 2025) |
| EllapsedTime: 852.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... 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 whether startup messages can be suppressed ... NOTE
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-27 20:26:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:30] [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
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-27 20:26:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:26:36] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 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: uniprot_full_id_mapping_table
> ### Title: Creates an ID translation table from UniProt data
> ### Aliases: uniprot_full_id_mapping_table
>
> ### ** Examples
>
> uniprot_entrez <- uniprot_full_id_mapping_table(to = 'entrez')
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE, :
Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Calls: uniprot_full_id_mapping_table ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 35.374 0.039 37.093
curated_ligrec_stats 9.290 0.480 83.396
omnipath-interactions 7.770 0.409 45.884
filter_extra_attrs 6.280 0.038 8.048
nichenet_gr_network_omnipath 5.201 0.292 7.981
pivot_annotations 4.153 0.274 25.299
extra_attrs_to_cols 4.229 0.059 5.618
nichenet_signaling_network_omnipath 3.775 0.228 10.919
extra_attr_values 3.603 0.064 8.925
giant_component 3.224 0.118 9.617
filter_by_resource 2.957 0.054 7.103
static_table 2.725 0.142 9.643
omnipath_for_cosmos 2.722 0.078 16.628
translate_ids_multi 2.463 0.108 13.648
filter_intercell 2.248 0.127 7.143
print_interactions 1.829 0.093 7.901
curated_ligand_receptor_interactions 1.677 0.141 13.863
ensembl_id_mapping_table 0.676 0.042 12.138
translate_ids 0.327 0.040 18.610
all_uniprots 0.252 0.035 110.254
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.0’ ** 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 [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Contains 1 files. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-27 15:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:36] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Contains 1 files. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-27 15:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-27 15:17:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/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)
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:39:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Contains 17 files.
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-27 20:39:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-27 20:39:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-27 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-27 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-27 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-27 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-27 20:39:51] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
3.616 0.403 35.643
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.005 | 0.001 | 0.007 | |
| all_uniprots | 0.252 | 0.035 | 110.254 | |
| ancestors | 0.003 | 0.000 | 0.002 | |
| annotated_network | 0.220 | 0.026 | 3.631 | |
| annotation_categories | 35.374 | 0.039 | 37.093 | |
| annotation_resources | 0.018 | 0.002 | 0.666 | |
| annotations | 0.074 | 0.007 | 1.080 | |
| biomart_query | 0.417 | 0.034 | 3.391 | |
| bioplex1 | 0.003 | 0.000 | 0.003 | |
| bioplex2 | 0.002 | 0.000 | 0.002 | |
| bioplex3 | 0.002 | 0.000 | 0.002 | |
| bioplex_all | 0.019 | 0.000 | 0.019 | |
| bioplex_hct116_1 | 0.002 | 0.000 | 0.003 | |
| bma_motif_es | 0.092 | 0.011 | 1.081 | |
| bma_motif_vs | 0.058 | 0.002 | 0.625 | |
| chalmers_gem | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_id_mapping_table | 0.002 | 0.001 | 0.003 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_network | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_raw | 0.003 | 0.001 | 0.007 | |
| chalmers_gem_reactions | 0.002 | 0.000 | 0.003 | |
| common_name | 0.008 | 0.000 | 0.008 | |
| complex_genes | 0.177 | 0.012 | 2.101 | |
| complex_resources | 0.020 | 0.003 | 0.808 | |
| complexes | 0.072 | 0.003 | 0.673 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.002 | 0.000 | 0.002 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 1.677 | 0.141 | 13.863 | |
| curated_ligrec_stats | 9.290 | 0.480 | 83.396 | |
| database_summary | 0.464 | 0.014 | 3.339 | |
| descendants | 0.003 | 0.001 | 0.003 | |
| ensembl_dataset | 0.004 | 0.000 | 0.004 | |
| ensembl_id_mapping_table | 0.676 | 0.042 | 12.138 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.015 | 0.000 | 0.016 | |
| ensembl_organisms | 0.034 | 0.001 | 0.035 | |
| ensembl_organisms_raw | 0.069 | 0.001 | 0.070 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 0.777 | 0.032 | 3.540 | |
| enzsub_resources | 0.019 | 0.002 | 0.667 | |
| enzyme_substrate | 0.330 | 0.006 | 0.875 | |
| evex_download | 0.003 | 0.000 | 0.003 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 3.603 | 0.064 | 8.925 | |
| extra_attrs | 2.512 | 0.013 | 3.804 | |
| extra_attrs_to_cols | 4.229 | 0.059 | 5.618 | |
| filter_by_resource | 2.957 | 0.054 | 7.103 | |
| filter_extra_attrs | 6.280 | 0.038 | 8.048 | |
| filter_intercell | 2.248 | 0.127 | 7.143 | |
| filter_intercell_network | 0.005 | 0.000 | 0.005 | |
| find_all_paths | 1.807 | 0.060 | 1.875 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.002 | 0.000 | 0.003 | |
| giant_component | 3.224 | 0.118 | 9.617 | |
| go_annot_download | 4.386 | 0.251 | 4.535 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.002 | 0.000 | 0.002 | |
| guide2pharma_download | 0.002 | 0.001 | 0.003 | |
| harmonizome_download | 0.002 | 0.000 | 0.002 | |
| has_extra_attrs | 1.917 | 0.024 | 1.948 | |
| hmdb_id_mapping_table | 0.014 | 0.000 | 0.014 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.002 | 0.000 | 0.003 | |
| homologene_download | 0.002 | 0.000 | 0.002 | |
| homologene_raw | 0.006 | 0.001 | 0.006 | |
| homologene_uniprot_orthology | 0.002 | 0.000 | 0.002 | |
| hpo_download | 0.876 | 0.076 | 1.373 | |
| htridb_download | 0.002 | 0.000 | 0.003 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.011 | 0.000 | 0.012 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.085 | 0.006 | 0.340 | |
| interaction_graph | 0.126 | 0.003 | 0.659 | |
| interaction_resources | 0.022 | 0.004 | 0.670 | |
| interaction_types | 0.012 | 0.000 | 0.014 | |
| intercell | 0.116 | 0.014 | 0.713 | |
| intercell_categories | 0.098 | 0.012 | 0.356 | |
| intercell_consensus_filter | 0.425 | 0.035 | 3.118 | |
| intercell_generic_categories | 0.012 | 0.000 | 0.014 | |
| intercell_network | 0.003 | 0.001 | 0.002 | |
| intercell_resources | 0.020 | 0.002 | 0.674 | |
| intercell_summary | 0.017 | 0.005 | 0.022 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.009 | 0.001 | 0.009 | |
| is_trembl | 0.007 | 0.000 | 0.008 | |
| is_uniprot | 0.003 | 0.001 | 0.003 | |
| kegg_info | 0.002 | 0.000 | 0.002 | |
| kegg_open | 0.002 | 0.000 | 0.002 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.002 | 0.000 | 0.003 | |
| kegg_pathway_list | 0.002 | 0.000 | 0.002 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.019 | 0.003 | 4.422 | |
| kegg_process | 0.004 | 0.001 | 0.005 | |
| latin_name | 0.031 | 0.001 | 0.032 | |
| load_db | 0.020 | 0.000 | 0.021 | |
| ncbi_taxid | 0.016 | 0.000 | 0.016 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network | 0.006 | 0.000 | 0.007 | |
| nichenet_gr_network_evex | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_harmonizome | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_htridb | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_omnipath | 5.201 | 0.292 | 7.981 | |
| nichenet_gr_network_pathwaycommons | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_regnetwork | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_remap | 0.002 | 0.000 | 0.002 | |
| nichenet_gr_network_trrust | 0.002 | 0.000 | 0.002 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.006 | 0.000 | 0.006 | |
| nichenet_lr_network_guide2pharma | 0.003 | 0.000 | 0.002 | |
| nichenet_lr_network_omnipath | 0.005 | 0.000 | 0.006 | |
| nichenet_lr_network_ramilowski | 0.002 | 0.000 | 0.003 | |
| nichenet_main | 0.000 | 0.001 | 0.000 | |
| nichenet_networks | 0.010 | 0.001 | 0.011 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.006 | 0.000 | 0.006 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.006 | 0.001 | 0.006 | |
| nichenet_signaling_network_cpdb | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_evex | 0.002 | 0.000 | 0.002 | |
| nichenet_signaling_network_harmonizome | 0.002 | 0.000 | 0.002 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 3.775 | 0.228 | 10.919 | |
| nichenet_signaling_network_pathwaycommons | 0.002 | 0.000 | 0.003 | |
| nichenet_signaling_network_vinayagam | 0.002 | 0.000 | 0.002 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.024 | 0.003 | 0.207 | |
| oma_code | 0.008 | 0.000 | 0.008 | |
| oma_organisms | 0.030 | 0.001 | 0.030 | |
| oma_pairwise | 0.003 | 0.000 | 0.003 | |
| oma_pairwise_genesymbols | 0.003 | 0.001 | 0.003 | |
| oma_pairwise_translated | 0.004 | 0.000 | 0.004 | |
| omnipath-interactions | 7.770 | 0.409 | 45.884 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.001 | 0.000 | 0.002 | |
| omnipath_cache_clean_db | 0.023 | 0.003 | 0.028 | |
| omnipath_cache_download_ready | 0.127 | 0.015 | 0.188 | |
| omnipath_cache_filter_versions | 0.022 | 0.004 | 0.045 | |
| omnipath_cache_get | 0.018 | 0.003 | 0.021 | |
| omnipath_cache_key | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.012 | 0.002 | 0.015 | |
| omnipath_cache_load | 0.210 | 0.011 | 3.150 | |
| omnipath_cache_move_in | 0.039 | 0.007 | 0.049 | |
| omnipath_cache_remove | 0.022 | 0.003 | 0.030 | |
| omnipath_cache_save | 0.036 | 0.005 | 0.057 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.018 | 0.003 | 0.025 | |
| omnipath_cache_update_status | 0.019 | 0.002 | 0.021 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.000 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 2.722 | 0.078 | 16.628 | |
| omnipath_load_config | 0.000 | 0.001 | 0.000 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.000 | 0.000 | 0.001 | |
| omnipath_msg | 0.002 | 0.000 | 0.001 | |
| omnipath_query | 1.199 | 0.019 | 1.217 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.025 | 0.001 | 0.026 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.017 | 0.001 | 0.017 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.000 | |
| ontology_ensure_name | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.000 | 0.001 | 0.000 | |
| organism_for | 0.014 | 0.000 | 0.014 | |
| pathwaycommons_download | 0.000 | 0.000 | 0.001 | |
| pivot_annotations | 4.153 | 0.274 | 25.299 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.061 | 0.013 | 0.932 | |
| print_bma_motif_vs | 0.033 | 0.002 | 0.639 | |
| print_interactions | 1.829 | 0.093 | 7.901 | |
| print_path_es | 0.152 | 0.015 | 1.730 | |
| print_path_vs | 0.712 | 0.046 | 3.382 | |
| pubmed_open | 1.226 | 0.024 | 1.261 | |
| query_info | 0.024 | 0.003 | 0.308 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| ramp_id_type | 0.001 | 0.000 | 0.001 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.023 | 0.001 | 0.047 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.018 | 0.001 | 0.032 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.001 | 0.000 | 0.000 | |
| resource_info | 0.041 | 0.016 | 0.717 | |
| resources | 0.016 | 0.003 | 0.806 | |
| resources_colname | 0.248 | 0.015 | 2.335 | |
| resources_in | 1.080 | 0.010 | 1.091 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 1.576 | 0.033 | 2.217 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 2.725 | 0.142 | 9.643 | |
| static_tables | 0.013 | 0.001 | 0.018 | |
| stitch_actions | 0.001 | 0.000 | 0.000 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0.002 | 0.001 | 0.002 | |
| swap_relations | 0.021 | 0.001 | 0.040 | |
| swissprots_only | 0.009 | 0.000 | 0.008 | |
| tfcensus_download | 0.046 | 0.006 | 0.195 | |
| translate_ids | 0.327 | 0.040 | 18.610 | |
| translate_ids_multi | 2.463 | 0.108 | 13.648 | |
| trembls_only | 0.009 | 0.000 | 0.009 | |
| trrust_download | 0 | 0 | 0 | |