Denes Turei
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:08 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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 | OK | 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: 2025-02-04 07:28:33 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 07:49:43 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 1270.2 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 4.4.2 (2024-10-31)
* 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
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 07:29:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:19] [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
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 07:29:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:29:49] [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 101.795 0.292 104.545
curated_ligrec_stats 58.197 1.654 120.019
omnipath-interactions 55.098 2.181 105.062
filter_extra_attrs 51.233 0.199 53.618
extra_attr_values 28.551 0.416 30.941
nichenet_gr_network_omnipath 26.356 1.220 29.502
extra_attrs_to_cols 25.220 0.169 26.116
with_extra_attrs 21.663 0.350 32.199
giant_component 21.011 0.431 22.754
nichenet_signaling_network_omnipath 18.927 0.615 20.934
go_annot_download 16.998 1.729 17.665
pivot_annotations 16.663 1.671 21.702
omnipath_for_cosmos 17.595 0.441 54.764
has_extra_attrs 15.898 0.115 16.545
extra_attrs 15.865 0.081 16.722
translate_ids_multi 14.155 0.328 46.116
filter_by_resource 13.592 0.256 15.116
find_all_paths 12.907 0.173 13.609
print_interactions 12.519 0.370 15.498
signed_ptms 11.428 0.058 12.510
static_table 9.870 0.740 11.188
filter_intercell 9.086 0.723 10.541
curated_ligand_receptor_interactions 9.372 0.382 17.065
omnipath_query 9.339 0.116 17.292
pubmed_open 8.647 0.077 8.893
resources_in 8.667 0.052 8.878
enzsub_graph 4.631 0.122 6.060
print_path_vs 4.583 0.149 6.891
ensembl_id_mapping_table 1.835 0.158 22.113
translate_ids 1.546 0.164 21.874
all_uniprots 1.468 0.152 30.164
uniprot_full_id_mapping_table 1.362 0.130 23.830
obo_parser 0.178 0.011 6.283
relations_list_to_table 0.156 0.009 6.389
* 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 [2025-02-03 16:07:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 16:07:31] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:31] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 16:07:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 16:07:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 16:07:32] [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). [2025-02-03 16:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:32] [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). [2025-02-03 16:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:32] [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). [2025-02-03 16:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:32] [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). [2025-02-03 16:07:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:32] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-03 16:07:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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)
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Contains 21 files.
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-04 07:48:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 07:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 07:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 07:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 07:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 07:48:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 07:48:26] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
21.555 1.638 51.453
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.002 | |
| all_uniprot_acs | 0.037 | 0.006 | 0.045 | |
| all_uniprots | 1.468 | 0.152 | 30.164 | |
| ancestors | 0.017 | 0.001 | 0.018 | |
| annotated_network | 1.374 | 0.094 | 3.731 | |
| annotation_categories | 101.795 | 0.292 | 104.545 | |
| annotation_resources | 0.124 | 0.008 | 0.831 | |
| annotations | 0.476 | 0.028 | 1.432 | |
| biomart_query | 1.427 | 0.153 | 3.502 | |
| bioplex1 | 0.018 | 0.002 | 0.020 | |
| bioplex2 | 0.018 | 0.001 | 0.020 | |
| bioplex3 | 0.019 | 0.001 | 0.021 | |
| bioplex_all | 0.018 | 0.002 | 0.019 | |
| bioplex_hct116_1 | 0.018 | 0.002 | 0.019 | |
| bma_motif_es | 0.632 | 0.044 | 1.587 | |
| bma_motif_vs | 0.359 | 0.010 | 0.885 | |
| chalmers_gem | 0.019 | 0.001 | 0.020 | |
| chalmers_gem_id_mapping_table | 0.019 | 0.001 | 0.021 | |
| chalmers_gem_id_type | 0.004 | 0.001 | 0.005 | |
| chalmers_gem_metabolites | 0.020 | 0.002 | 0.020 | |
| chalmers_gem_network | 0.018 | 0.002 | 0.020 | |
| chalmers_gem_raw | 0.019 | 0.002 | 0.019 | |
| chalmers_gem_reactions | 0.018 | 0.002 | 0.020 | |
| common_name | 0.055 | 0.001 | 0.057 | |
| complex_genes | 0.812 | 0.044 | 2.242 | |
| complex_resources | 0.127 | 0.004 | 0.758 | |
| complexes | 0.306 | 0.008 | 0.808 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.020 | 0.002 | 0.021 | |
| cosmos_pkn | 0.000 | 0.001 | 0.001 | |
| curated_ligand_receptor_interactions | 9.372 | 0.382 | 17.065 | |
| curated_ligrec_stats | 58.197 | 1.654 | 120.019 | |
| database_summary | 2.712 | 0.050 | 3.723 | |
| descendants | 0.018 | 0.002 | 0.019 | |
| ensembl_dataset | 0.018 | 0.001 | 0.019 | |
| ensembl_id_mapping_table | 1.835 | 0.158 | 22.113 | |
| ensembl_id_type | 0.004 | 0.001 | 0.007 | |
| ensembl_name | 0.160 | 0.003 | 0.173 | |
| ensembl_organisms | 0.271 | 0.005 | 0.308 | |
| ensembl_organisms_raw | 0.294 | 0.006 | 0.301 | |
| ensembl_orthology | 0.000 | 0.002 | 0.002 | |
| enzsub_graph | 4.631 | 0.122 | 6.060 | |
| enzsub_resources | 0.124 | 0.006 | 0.811 | |
| enzyme_substrate | 2.406 | 0.017 | 2.948 | |
| evex_download | 0.018 | 0.002 | 0.020 | |
| evidences | 0.001 | 0.001 | 0.001 | |
| extra_attr_values | 28.551 | 0.416 | 30.941 | |
| extra_attrs | 15.865 | 0.081 | 16.722 | |
| extra_attrs_to_cols | 25.220 | 0.169 | 26.116 | |
| filter_by_resource | 13.592 | 0.256 | 15.116 | |
| filter_extra_attrs | 51.233 | 0.199 | 53.618 | |
| filter_intercell | 9.086 | 0.723 | 10.541 | |
| filter_intercell_network | 0.040 | 0.003 | 0.047 | |
| find_all_paths | 12.907 | 0.173 | 13.609 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.000 | 0.001 | 0.001 | |
| get_ontology_db | 0.019 | 0.003 | 0.021 | |
| giant_component | 21.011 | 0.431 | 22.754 | |
| go_annot_download | 16.998 | 1.729 | 17.665 | |
| go_annot_slim | 0.000 | 0.001 | 0.001 | |
| go_ontology_download | 0.019 | 0.001 | 0.020 | |
| guide2pharma_download | 0.018 | 0.002 | 0.021 | |
| harmonizome_download | 0.018 | 0.001 | 0.020 | |
| has_extra_attrs | 15.898 | 0.115 | 16.545 | |
| hmdb_id_mapping_table | 0.021 | 0.002 | 0.024 | |
| hmdb_id_type | 0.005 | 0.001 | 0.005 | |
| hmdb_metabolite_fields | 0.000 | 0.002 | 0.003 | |
| hmdb_protein_fields | 0.001 | 0.002 | 0.002 | |
| hmdb_table | 0.017 | 0.001 | 0.020 | |
| homologene_download | 0.019 | 0.002 | 0.021 | |
| homologene_raw | 0.036 | 0.003 | 0.041 | |
| homologene_uniprot_orthology | 0.018 | 0.002 | 0.021 | |
| hpo_download | 3.561 | 0.389 | 4.000 | |
| htridb_download | 0.017 | 0.002 | 0.059 | |
| id_translation_resources | 0.001 | 0.000 | 0.001 | |
| id_types | 0.078 | 0.001 | 0.081 | |
| inbiomap_download | 0.001 | 0.001 | 0.002 | |
| inbiomap_raw | 0.000 | 0.001 | 0.001 | |
| interaction_datasets | 0.668 | 0.055 | 1.145 | |
| interaction_graph | 0.772 | 0.010 | 1.247 | |
| interaction_resources | 0.171 | 0.010 | 0.770 | |
| interaction_types | 0.081 | 0.004 | 0.085 | |
| intercell | 0.770 | 0.052 | 1.305 | |
| intercell_categories | 0.673 | 0.065 | 1.031 | |
| intercell_consensus_filter | 2.006 | 0.174 | 2.822 | |
| intercell_generic_categories | 0.084 | 0.004 | 0.090 | |
| intercell_network | 0.020 | 0.001 | 0.021 | |
| intercell_resources | 0.125 | 0.005 | 0.621 | |
| intercell_summary | 0.095 | 0.032 | 0.129 | |
| is_ontology_id | 0.000 | 0.001 | 0.001 | |
| is_swissprot | 0.054 | 0.003 | 0.057 | |
| is_trembl | 0.100 | 0.008 | 0.110 | |
| is_uniprot | 0.021 | 0.002 | 0.023 | |
| kegg_info | 0.018 | 0.001 | 0.019 | |
| kegg_open | 0.018 | 0.001 | 0.020 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.022 | 0.001 | 0.024 | |
| kegg_pathway_list | 0.020 | 0.002 | 0.065 | |
| kegg_pathways_download | 0.001 | 0.001 | 0.001 | |
| kegg_picture | 0.115 | 0.012 | 2.017 | |
| kegg_process | 0.036 | 0.003 | 0.039 | |
| latin_name | 0.104 | 0.000 | 0.105 | |
| load_db | 0.145 | 0.004 | 0.152 | |
| ncbi_taxid | 0.107 | 0.001 | 0.109 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.019 | 0.002 | 0.021 | |
| nichenet_gr_network | 0.099 | 0.003 | 0.104 | |
| nichenet_gr_network_evex | 0.019 | 0.001 | 0.020 | |
| nichenet_gr_network_harmonizome | 0.018 | 0.001 | 0.020 | |
| nichenet_gr_network_htridb | 0.018 | 0.001 | 0.020 | |
| nichenet_gr_network_omnipath | 26.356 | 1.220 | 29.502 | |
| nichenet_gr_network_pathwaycommons | 0.019 | 0.002 | 0.021 | |
| nichenet_gr_network_regnetwork | 0.019 | 0.001 | 0.021 | |
| nichenet_gr_network_remap | 0.019 | 0.002 | 0.022 | |
| nichenet_gr_network_trrust | 0.018 | 0.002 | 0.024 | |
| nichenet_ligand_activities | 0.001 | 0.002 | 0.001 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_matrix | 0.000 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.056 | 0.004 | 0.065 | |
| nichenet_lr_network_guide2pharma | 0.019 | 0.002 | 0.022 | |
| nichenet_lr_network_omnipath | 0.092 | 0.007 | 0.104 | |
| nichenet_lr_network_ramilowski | 0.018 | 0.001 | 0.021 | |
| nichenet_main | 0.001 | 0.002 | 0.002 | |
| nichenet_networks | 0.093 | 0.008 | 0.111 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.054 | 0.002 | 0.063 | |
| nichenet_results_dir | 0.000 | 0.001 | 0.001 | |
| nichenet_signaling_network | 0.057 | 0.003 | 0.064 | |
| nichenet_signaling_network_cpdb | 0.017 | 0.001 | 0.020 | |
| nichenet_signaling_network_evex | 0.019 | 0.001 | 0.021 | |
| nichenet_signaling_network_harmonizome | 0.018 | 0.001 | 0.021 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.001 | 0.000 | |
| nichenet_signaling_network_omnipath | 18.927 | 0.615 | 20.934 | |
| nichenet_signaling_network_pathwaycommons | 0.018 | 0.002 | 0.022 | |
| nichenet_signaling_network_vinayagam | 0.051 | 0.005 | 0.059 | |
| nichenet_test | 0.001 | 0.001 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.178 | 0.011 | 6.283 | |
| oma_code | 0.055 | 0.002 | 0.073 | |
| oma_organisms | 0.094 | 0.003 | 0.130 | |
| oma_pairwise | 0.018 | 0.002 | 0.022 | |
| oma_pairwise_genesymbols | 0.018 | 0.002 | 0.020 | |
| oma_pairwise_translated | 0.018 | 0.002 | 0.026 | |
| omnipath-interactions | 55.098 | 2.181 | 105.062 | |
| omnipath_cache_autoclean | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.017 | 0.002 | 0.030 | |
| omnipath_cache_clean_db | 0.245 | 0.014 | 0.520 | |
| omnipath_cache_download_ready | 0.983 | 0.079 | 2.167 | |
| omnipath_cache_filter_versions | 0.185 | 0.021 | 0.455 | |
| omnipath_cache_get | 0.166 | 0.019 | 0.359 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.003 | |
| omnipath_cache_latest_or_new | 0.116 | 0.014 | 0.253 | |
| omnipath_cache_load | 1.051 | 0.056 | 2.920 | |
| omnipath_cache_move_in | 0.297 | 0.033 | 0.740 | |
| omnipath_cache_remove | 0.183 | 0.020 | 0.507 | |
| omnipath_cache_save | 0.277 | 0.027 | 0.613 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.011 | |
| omnipath_cache_set_ext | 0.147 | 0.016 | 0.354 | |
| omnipath_cache_update_status | 0.200 | 0.023 | 0.442 | |
| omnipath_cache_wipe | 0.001 | 0.000 | 0.011 | |
| omnipath_config_path | 0.000 | 0.001 | 0.002 | |
| omnipath_for_cosmos | 17.595 | 0.441 | 54.764 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0.001 | 0.001 | 0.000 | |
| omnipath_logfile | 0.003 | 0.001 | 0.004 | |
| omnipath_msg | 0.010 | 0.002 | 0.020 | |
| omnipath_query | 9.339 | 0.116 | 17.292 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.001 | |
| omnipath_save_config | 0.000 | 0.000 | 0.001 | |
| omnipath_set_cachedir | 0.050 | 0.005 | 0.105 | |
| omnipath_set_console_loglevel | 0.007 | 0.001 | 0.018 | |
| omnipath_set_logfile_loglevel | 0.008 | 0.001 | 0.014 | |
| omnipath_set_loglevel | 0.004 | 0.001 | 0.004 | |
| omnipath_show_db | 0.106 | 0.001 | 0.194 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.010 | |
| only_from | 0.001 | 0.001 | 0.001 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.002 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.011 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.074 | 0.002 | 0.142 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.002 | |
| pivot_annotations | 16.663 | 1.671 | 21.702 | |
| preppi_download | 0.001 | 0.002 | 0.002 | |
| preppi_filter | 0.002 | 0.000 | 0.003 | |
| print_bma_motif_es | 0.364 | 0.051 | 1.207 | |
| print_bma_motif_vs | 0.223 | 0.005 | 0.844 | |
| print_interactions | 12.519 | 0.370 | 15.498 | |
| print_path_es | 0.908 | 0.050 | 1.984 | |
| print_path_vs | 4.583 | 0.149 | 6.891 | |
| pubmed_open | 8.647 | 0.077 | 8.893 | |
| query_info | 0.158 | 0.013 | 0.467 | |
| ramilowski_download | 0.000 | 0.001 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.004 | 0.001 | 0.004 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.001 | 0.001 | 0.002 | |
| regnetwork_directions | 0.001 | 0.002 | 0.002 | |
| regnetwork_download | 0.001 | 0.001 | 0.003 | |
| relations_list_to_table | 0.156 | 0.009 | 6.389 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.128 | 0.006 | 0.157 | |
| remap_dorothea_download | 0.001 | 0.001 | 0.002 | |
| remap_filtered | 0.000 | 0.001 | 0.002 | |
| remap_tf_target_download | 0.000 | 0.001 | 0.001 | |
| resource_info | 0.283 | 0.121 | 0.956 | |
| resources | 0.110 | 0.012 | 0.591 | |
| resources_colname | 0.893 | 0.085 | 1.760 | |
| resources_in | 8.667 | 0.052 | 8.878 | |
| show_network | 0.001 | 0.001 | 0.001 | |
| signed_ptms | 11.428 | 0.058 | 12.510 | |
| simplify_intercell_network | 0.002 | 0.001 | 0.002 | |
| static_table | 9.870 | 0.740 | 11.188 | |
| static_tables | 0.167 | 0.009 | 0.286 | |
| stitch_actions | 0.001 | 0.001 | 0.002 | |
| stitch_links | 0.001 | 0.000 | 0.002 | |
| stitch_network | 0.001 | 0.001 | 0.002 | |
| stitch_remove_prefixes | 0.013 | 0.001 | 0.014 | |
| swap_relations | 0.145 | 0.006 | 0.172 | |
| swissprots_only | 0.058 | 0.000 | 0.059 | |
| tfcensus_download | 0.290 | 0.022 | 0.505 | |
| translate_ids | 1.546 | 0.164 | 21.874 | |
| translate_ids_multi | 14.155 | 0.328 | 46.116 | |
| trembls_only | 0.056 | 0.001 | 0.059 | |
| trrust_download | 0.001 | 0.000 | 0.002 | |
| uniprot_full_id_mapping_table | 1.362 | 0.130 | 23.830 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.002 | |
| uniprot_id_type | 0.004 | 0.001 | 0.013 | |
| uniprot_idmapping_id_types | 0.324 | 0.028 | 0.958 | |
| unique_intercell_network | 0.002 | 0.001 | 0.002 | |
| unnest_evidences | 0.000 | 0.001 | 0.000 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.005 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.002 | 0.001 | 0.005 | |
| with_extra_attrs | 21.663 | 0.350 | 32.199 | |
| with_references | 0.804 | 0.050 | 1.848 | |
| zenodo_download | 0.002 | 0.001 | 0.004 | |