Denes Turei
| Snapshot Date: 2025-03-13 13:00 -0400 (Thu, 13 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-17 12:09 -0400 (Mon, 17 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4399 |
| 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 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 3.14.0 |
| 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_3.14.0.tar.gz |
| StartedAt: 2025-03-14 06:32:56 -0400 (Fri, 14 Mar 2025) |
| EndedAt: 2025-03-14 06:54:21 -0400 (Fri, 14 Mar 2025) |
| EllapsedTime: 1285.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 ... 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
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 06:33:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:33:41] [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
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 06:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:34:11] [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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 101.872 0.312 104.745
curated_ligrec_stats 58.577 1.642 120.439
omnipath-interactions 55.370 1.650 113.357
filter_extra_attrs 52.456 0.202 54.877
extra_attr_values 28.907 0.468 31.487
nichenet_gr_network_omnipath 25.043 1.062 27.437
extra_attrs_to_cols 25.140 0.125 26.368
giant_component 20.969 0.443 22.452
with_extra_attrs 20.950 0.309 22.719
nichenet_signaling_network_omnipath 19.854 0.592 21.941
go_annot_download 17.334 1.725 17.596
pivot_annotations 16.264 1.341 19.617
omnipath_for_cosmos 17.162 0.358 43.344
has_extra_attrs 15.839 0.108 16.362
extra_attrs 15.632 0.062 15.772
filter_by_resource 13.654 0.263 15.034
translate_ids_multi 13.406 0.248 35.686
print_interactions 12.564 0.293 19.590
find_all_paths 12.416 0.173 13.442
signed_ptms 11.774 0.067 21.053
static_table 9.632 0.776 22.304
curated_ligand_receptor_interactions 9.476 0.389 16.883
filter_intercell 9.146 0.681 10.541
omnipath_query 9.239 0.129 9.784
resources_in 9.049 0.045 17.717
pubmed_open 8.764 0.085 9.636
print_path_vs 4.951 0.165 10.382
enzsub_graph 4.581 0.114 6.089
translate_ids 1.761 0.146 21.944
ensembl_id_mapping_table 1.735 0.150 26.202
biomart_query 1.481 0.159 6.235
all_uniprots 1.470 0.148 25.049
uniprot_full_id_mapping_table 1.394 0.078 25.435
omnipath_cache_load 0.972 0.044 7.877
omnipath_cache_move_in 0.291 0.033 6.108
omnipath_cache_save 0.285 0.029 5.983
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/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 [2025-03-13 15:56:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 15:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:54] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:56:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 15:56:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:56:54] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 15:56:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 15:56:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 15:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:56:56] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-13 15:56:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 15:56:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 15:56:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 15:56:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 15:56:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:56:56] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 15:57:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 15:57:01] [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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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)
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:53:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:12] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Contains 21 files.
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-14 06:53:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 06:53:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 06:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 06:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 06:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 06:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-14 06:53:13] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
21.258 1.591 43.974
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.002 | 0.002 | |
| all_uniprot_acs | 0.037 | 0.006 | 0.042 | |
| all_uniprots | 1.470 | 0.148 | 25.049 | |
| ancestors | 0.017 | 0.001 | 0.018 | |
| annotated_network | 1.375 | 0.093 | 3.618 | |
| annotation_categories | 101.872 | 0.312 | 104.745 | |
| annotation_resources | 0.127 | 0.007 | 0.612 | |
| annotations | 0.501 | 0.026 | 1.302 | |
| biomart_query | 1.481 | 0.159 | 6.235 | |
| bioplex1 | 0.018 | 0.001 | 0.020 | |
| bioplex2 | 0.019 | 0.001 | 0.019 | |
| bioplex3 | 0.018 | 0.002 | 0.020 | |
| bioplex_all | 0.018 | 0.002 | 0.020 | |
| bioplex_hct116_1 | 0.018 | 0.001 | 0.019 | |
| bma_motif_es | 0.677 | 0.043 | 1.645 | |
| bma_motif_vs | 0.360 | 0.011 | 0.840 | |
| chalmers_gem | 0.018 | 0.001 | 0.020 | |
| chalmers_gem_id_mapping_table | 0.019 | 0.001 | 0.021 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.004 | |
| chalmers_gem_metabolites | 0.019 | 0.001 | 0.020 | |
| chalmers_gem_network | 0.019 | 0.002 | 0.020 | |
| chalmers_gem_raw | 0.018 | 0.002 | 0.020 | |
| chalmers_gem_reactions | 0.017 | 0.002 | 0.020 | |
| common_name | 0.053 | 0.000 | 0.054 | |
| complex_genes | 0.829 | 0.045 | 2.083 | |
| complex_resources | 0.129 | 0.005 | 0.597 | |
| complexes | 0.312 | 0.009 | 0.931 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.018 | 0.001 | 0.019 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 9.476 | 0.389 | 16.883 | |
| curated_ligrec_stats | 58.577 | 1.642 | 120.439 | |
| database_summary | 2.735 | 0.049 | 3.703 | |
| descendants | 0.017 | 0.002 | 0.019 | |
| ensembl_dataset | 0.019 | 0.001 | 0.019 | |
| ensembl_id_mapping_table | 1.735 | 0.150 | 26.202 | |
| ensembl_id_type | 0.004 | 0.000 | 0.005 | |
| ensembl_name | 0.149 | 0.002 | 0.155 | |
| ensembl_organisms | 0.264 | 0.003 | 0.269 | |
| ensembl_organisms_raw | 0.295 | 0.006 | 0.305 | |
| ensembl_orthology | 0.001 | 0.001 | 0.001 | |
| enzsub_graph | 4.581 | 0.114 | 6.089 | |
| enzsub_resources | 0.129 | 0.006 | 0.868 | |
| enzyme_substrate | 2.409 | 0.019 | 3.179 | |
| evex_download | 0.020 | 0.003 | 0.022 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 28.907 | 0.468 | 31.487 | |
| extra_attrs | 15.632 | 0.062 | 15.772 | |
| extra_attrs_to_cols | 25.140 | 0.125 | 26.368 | |
| filter_by_resource | 13.654 | 0.263 | 15.034 | |
| filter_extra_attrs | 52.456 | 0.202 | 54.877 | |
| filter_intercell | 9.146 | 0.681 | 10.541 | |
| filter_intercell_network | 0.039 | 0.002 | 0.044 | |
| find_all_paths | 12.416 | 0.173 | 13.442 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.001 | 0.001 | 0.001 | |
| get_ontology_db | 0.019 | 0.002 | 0.021 | |
| giant_component | 20.969 | 0.443 | 22.452 | |
| go_annot_download | 17.334 | 1.725 | 17.596 | |
| go_annot_slim | 0.001 | 0.002 | 0.002 | |
| go_ontology_download | 0.017 | 0.001 | 0.019 | |
| guide2pharma_download | 0.018 | 0.002 | 0.020 | |
| harmonizome_download | 0.018 | 0.001 | 0.019 | |
| has_extra_attrs | 15.839 | 0.108 | 16.362 | |
| hmdb_id_mapping_table | 0.018 | 0.002 | 0.020 | |
| hmdb_id_type | 0.004 | 0.000 | 0.006 | |
| hmdb_metabolite_fields | 0.001 | 0.002 | 0.003 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.002 | |
| hmdb_table | 0.018 | 0.002 | 0.019 | |
| homologene_download | 0.017 | 0.002 | 0.019 | |
| homologene_raw | 0.035 | 0.003 | 0.038 | |
| homologene_uniprot_orthology | 0.019 | 0.003 | 0.021 | |
| hpo_download | 3.597 | 0.404 | 4.177 | |
| htridb_download | 0.018 | 0.002 | 0.021 | |
| id_translation_resources | 0.001 | 0.001 | 0.001 | |
| id_types | 0.079 | 0.002 | 0.082 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0.001 | 0.000 | 0.001 | |
| interaction_datasets | 0.650 | 0.036 | 1.155 | |
| interaction_graph | 0.785 | 0.011 | 1.370 | |
| interaction_resources | 0.131 | 0.011 | 0.741 | |
| interaction_types | 0.080 | 0.004 | 0.083 | |
| intercell | 0.775 | 0.055 | 1.301 | |
| intercell_categories | 0.689 | 0.066 | 1.036 | |
| intercell_consensus_filter | 1.988 | 0.160 | 2.822 | |
| intercell_generic_categories | 0.084 | 0.005 | 0.092 | |
| intercell_network | 0.019 | 0.002 | 0.021 | |
| intercell_resources | 0.128 | 0.004 | 0.599 | |
| intercell_summary | 0.094 | 0.033 | 0.131 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.053 | 0.002 | 0.058 | |
| is_trembl | 0.052 | 0.003 | 0.057 | |
| is_uniprot | 0.019 | 0.002 | 0.020 | |
| kegg_info | 0.070 | 0.005 | 0.079 | |
| kegg_open | 0.020 | 0.001 | 0.022 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.019 | 0.002 | 0.023 | |
| kegg_pathway_list | 0.019 | 0.002 | 0.021 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
| kegg_picture | 0.116 | 0.012 | 1.854 | |
| kegg_process | 0.035 | 0.003 | 0.037 | |
| latin_name | 0.102 | 0.002 | 0.104 | |
| load_db | 0.140 | 0.004 | 0.151 | |
| ncbi_taxid | 0.102 | 0.001 | 0.106 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.018 | 0.002 | 0.022 | |
| nichenet_gr_network | 0.053 | 0.004 | 0.061 | |
| nichenet_gr_network_evex | 0.018 | 0.002 | 0.020 | |
| nichenet_gr_network_harmonizome | 0.019 | 0.002 | 0.021 | |
| nichenet_gr_network_htridb | 0.018 | 0.001 | 0.020 | |
| nichenet_gr_network_omnipath | 25.043 | 1.062 | 27.437 | |
| nichenet_gr_network_pathwaycommons | 0.019 | 0.002 | 0.020 | |
| nichenet_gr_network_regnetwork | 0.019 | 0.001 | 0.021 | |
| nichenet_gr_network_remap | 0.017 | 0.001 | 0.019 | |
| nichenet_gr_network_trrust | 0.019 | 0.002 | 0.020 | |
| nichenet_ligand_activities | 0.000 | 0.002 | 0.002 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_matrix | 0.001 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.058 | 0.004 | 0.063 | |
| nichenet_lr_network_guide2pharma | 0.020 | 0.001 | 0.021 | |
| nichenet_lr_network_omnipath | 0.104 | 0.005 | 0.110 | |
| nichenet_lr_network_ramilowski | 0.018 | 0.001 | 0.020 | |
| nichenet_main | 0.000 | 0.001 | 0.001 | |
| nichenet_networks | 0.087 | 0.008 | 0.097 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.054 | 0.003 | 0.058 | |
| nichenet_results_dir | 0.001 | 0.001 | 0.001 | |
| nichenet_signaling_network | 0.057 | 0.005 | 0.077 | |
| nichenet_signaling_network_cpdb | 0.018 | 0.001 | 0.019 | |
| nichenet_signaling_network_evex | 0.018 | 0.001 | 0.020 | |
| nichenet_signaling_network_harmonizome | 0.018 | 0.001 | 0.020 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 19.854 | 0.592 | 21.941 | |
| nichenet_signaling_network_pathwaycommons | 0.018 | 0.002 | 0.019 | |
| nichenet_signaling_network_vinayagam | 0.017 | 0.001 | 0.019 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.167 | 0.010 | 0.211 | |
| oma_code | 0.053 | 0.001 | 0.055 | |
| oma_organisms | 0.091 | 0.002 | 0.095 | |
| oma_pairwise | 0.018 | 0.002 | 0.019 | |
| oma_pairwise_genesymbols | 0.018 | 0.001 | 0.020 | |
| oma_pairwise_translated | 0.017 | 0.001 | 0.019 | |
| omnipath-interactions | 55.370 | 1.650 | 113.357 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.015 | 0.001 | 0.016 | |
| omnipath_cache_clean_db | 0.193 | 0.010 | 0.325 | |
| omnipath_cache_download_ready | 1.057 | 0.082 | 2.537 | |
| omnipath_cache_filter_versions | 0.187 | 0.020 | 0.503 | |
| omnipath_cache_get | 0.163 | 0.017 | 0.659 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.003 | |
| omnipath_cache_latest_or_new | 0.115 | 0.015 | 1.352 | |
| omnipath_cache_load | 0.972 | 0.044 | 7.877 | |
| omnipath_cache_move_in | 0.291 | 0.033 | 6.108 | |
| omnipath_cache_remove | 0.180 | 0.020 | 3.899 | |
| omnipath_cache_save | 0.285 | 0.029 | 5.983 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.153 | 0.016 | 3.560 | |
| omnipath_cache_update_status | 0.221 | 0.018 | 3.824 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.011 | |
| omnipath_for_cosmos | 17.162 | 0.358 | 43.344 | |
| omnipath_load_config | 0.000 | 0.001 | 0.001 | |
| omnipath_log | 0.001 | 0.000 | 0.001 | |
| omnipath_logfile | 0.003 | 0.001 | 0.004 | |
| omnipath_msg | 0.010 | 0.001 | 0.012 | |
| omnipath_query | 9.239 | 0.129 | 9.784 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.002 | |
| omnipath_save_config | 0.000 | 0.001 | 0.001 | |
| omnipath_set_cachedir | 0.048 | 0.005 | 0.053 | |
| omnipath_set_console_loglevel | 0.008 | 0.001 | 0.008 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.001 | 0.008 | |
| omnipath_set_loglevel | 0.004 | 0.000 | 0.004 | |
| omnipath_show_db | 0.157 | 0.002 | 0.160 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.001 | |
| only_from | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.002 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.002 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.070 | 0.001 | 0.072 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.002 | |
| pivot_annotations | 16.264 | 1.341 | 19.617 | |
| preppi_download | 0.001 | 0.001 | 0.002 | |
| preppi_filter | 0.002 | 0.001 | 0.002 | |
| print_bma_motif_es | 0.354 | 0.036 | 1.296 | |
| print_bma_motif_vs | 0.220 | 0.006 | 0.869 | |
| print_interactions | 12.564 | 0.293 | 19.590 | |
| print_path_es | 0.857 | 0.047 | 2.562 | |
| print_path_vs | 4.951 | 0.165 | 10.382 | |
| pubmed_open | 8.764 | 0.085 | 9.636 | |
| query_info | 0.156 | 0.012 | 0.476 | |
| ramilowski_download | 0.001 | 0.001 | 0.002 | |
| ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| ramp_id_type | 0.004 | 0.001 | 0.004 | |
| ramp_sqlite | 0.001 | 0.001 | 0.001 | |
| ramp_table | 0.001 | 0.001 | 0.001 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.001 | 0.003 | |
| regnetwork_download | 0.001 | 0.001 | 0.002 | |
| relations_list_to_table | 0.156 | 0.008 | 0.238 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.139 | 0.007 | 0.300 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.002 | |
| remap_filtered | 0.000 | 0.000 | 0.001 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.001 | |
| resource_info | 0.292 | 0.119 | 1.090 | |
| resources | 0.113 | 0.008 | 0.834 | |
| resources_colname | 0.911 | 0.087 | 2.485 | |
| resources_in | 9.049 | 0.045 | 17.717 | |
| show_network | 0.000 | 0.001 | 0.001 | |
| signed_ptms | 11.774 | 0.067 | 21.053 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.003 | |
| static_table | 9.632 | 0.776 | 22.304 | |
| static_tables | 0.089 | 0.002 | 0.220 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.001 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.001 | 0.014 | |
| stitch_remove_prefixes | 0.013 | 0.001 | 0.027 | |
| swap_relations | 0.151 | 0.007 | 0.330 | |
| swissprots_only | 0.060 | 0.001 | 0.129 | |
| tfcensus_download | 0.417 | 0.024 | 0.896 | |
| translate_ids | 1.761 | 0.146 | 21.944 | |
| translate_ids_multi | 13.406 | 0.248 | 35.686 | |
| trembls_only | 0.060 | 0.001 | 0.069 | |
| trrust_download | 0.001 | 0.001 | 0.002 | |
| uniprot_full_id_mapping_table | 1.394 | 0.078 | 25.435 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.000 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.002 | |
| uniprot_id_type | 0.004 | 0.000 | 0.005 | |
| uniprot_idmapping_id_types | 0.325 | 0.018 | 0.849 | |
| unique_intercell_network | 0.001 | 0.001 | 0.002 | |
| unnest_evidences | 0.001 | 0.001 | 0.001 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.005 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.002 | 0.001 | 0.004 | |
| with_extra_attrs | 20.950 | 0.309 | 22.719 | |
| with_references | 0.805 | 0.055 | 2.089 | |
| zenodo_download | 0.003 | 0.001 | 0.004 | |