Denes Turei
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 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 2025-04-02 19:32 -0400 (Wed, 02 Apr 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" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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: 2025-04-01 06:41:31 -0400 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 07:05:03 -0400 (Tue, 01 Apr 2025) |
| EllapsedTime: 1411.4 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
[2025-04-01 06:42:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 06:42:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:16] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-01 06:42:16] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:16] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 06:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-01 06:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-01 06:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-01 06:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-01 06:42:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:17] [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
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 06:42:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-01 06:42:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 06:42:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 06:42:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-01 06:42:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-01 06:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-01 06:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-01 06:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-01 06:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 06:42:47] [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 101.437 0.381 104.991
curated_ligrec_stats 60.849 1.682 121.446
omnipath-interactions 56.976 1.561 82.633
filter_extra_attrs 51.958 0.333 60.975
extra_attr_values 28.767 0.453 31.097
nichenet_gr_network_omnipath 26.777 1.008 30.422
extra_attrs_to_cols 25.290 0.100 26.069
go_annot_download 20.608 2.194 36.645
giant_component 22.048 0.477 43.889
with_extra_attrs 20.787 0.271 21.814
nichenet_signaling_network_omnipath 18.484 0.564 20.761
pivot_annotations 16.574 1.383 26.976
omnipath_for_cosmos 17.176 0.377 40.536
has_extra_attrs 16.286 0.151 24.450
extra_attrs 16.016 0.079 16.502
filter_by_resource 13.893 0.271 15.640
translate_ids_multi 13.246 0.215 28.959
print_interactions 12.895 0.308 15.658
find_all_paths 12.878 0.267 24.305
signed_ptms 11.856 0.053 13.083
static_table 9.687 0.728 14.156
filter_intercell 9.654 0.722 18.949
curated_ligand_receptor_interactions 9.681 0.375 17.683
pubmed_open 9.507 0.130 10.040
omnipath_query 9.475 0.060 18.446
resources_in 9.198 0.038 9.716
print_path_vs 4.630 0.095 6.586
enzsub_graph 4.389 0.104 6.074
translate_ids 1.839 0.132 20.135
ensembl_id_mapping_table 1.773 0.136 16.653
all_uniprots 1.549 0.158 95.614
uniprot_full_id_mapping_table 1.470 0.141 89.783
annotated_network 1.384 0.095 9.651
kegg_picture 0.116 0.012 8.052
* 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 [2025-03-31 15:58:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Contains 1 files. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-31 15:58:13] [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). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [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). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [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). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [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). [2025-03-31 15:58:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:13] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-31 15:58:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-31 15:58:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:18] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Contains 1 files. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-31 15:58:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-31 15:58:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-31 15:58:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-31 15:58:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-31 15:58:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-31 15:58:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-31 15:58:19] [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)
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Contains 21 files.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-01 07:03:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-01 07:03:54] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
21.246 1.516 43.689
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.002 | 0.002 | |
| all_uniprot_acs | 0.036 | 0.005 | 0.041 | |
| all_uniprots | 1.549 | 0.158 | 95.614 | |
| ancestors | 0.017 | 0.002 | 0.019 | |
| annotated_network | 1.384 | 0.095 | 9.651 | |
| annotation_categories | 101.437 | 0.381 | 104.991 | |
| annotation_resources | 0.129 | 0.007 | 0.645 | |
| annotations | 0.494 | 0.028 | 1.288 | |
| biomart_query | 1.484 | 0.163 | 2.591 | |
| bioplex1 | 0.018 | 0.001 | 0.019 | |
| bioplex2 | 0.019 | 0.002 | 0.020 | |
| bioplex3 | 0.017 | 0.001 | 0.019 | |
| bioplex_all | 0.019 | 0.002 | 0.021 | |
| bioplex_hct116_1 | 0.019 | 0.001 | 0.020 | |
| bma_motif_es | 0.697 | 0.044 | 1.763 | |
| bma_motif_vs | 0.318 | 0.011 | 0.820 | |
| chalmers_gem | 0.020 | 0.001 | 0.021 | |
| chalmers_gem_id_mapping_table | 0.018 | 0.001 | 0.020 | |
| chalmers_gem_id_type | 0.004 | 0.000 | 0.004 | |
| chalmers_gem_metabolites | 0.018 | 0.001 | 0.023 | |
| chalmers_gem_network | 0.019 | 0.001 | 0.023 | |
| chalmers_gem_raw | 0.019 | 0.001 | 0.022 | |
| chalmers_gem_reactions | 0.018 | 0.001 | 0.019 | |
| common_name | 0.055 | 0.001 | 0.060 | |
| complex_genes | 0.791 | 0.043 | 2.259 | |
| complex_resources | 0.165 | 0.006 | 0.652 | |
| complexes | 0.262 | 0.009 | 0.747 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.017 | 0.001 | 0.017 | |
| cosmos_pkn | 0.001 | 0.000 | 0.000 | |
| curated_ligand_receptor_interactions | 9.681 | 0.375 | 17.683 | |
| curated_ligrec_stats | 60.849 | 1.682 | 121.446 | |
| database_summary | 2.794 | 0.055 | 4.011 | |
| descendants | 0.019 | 0.001 | 0.022 | |
| ensembl_dataset | 0.019 | 0.001 | 0.020 | |
| ensembl_id_mapping_table | 1.773 | 0.136 | 16.653 | |
| ensembl_id_type | 0.004 | 0.000 | 0.006 | |
| ensembl_name | 0.209 | 0.005 | 0.222 | |
| ensembl_organisms | 0.263 | 0.003 | 0.280 | |
| ensembl_organisms_raw | 0.288 | 0.008 | 0.307 | |
| ensembl_orthology | 0.001 | 0.002 | 0.002 | |
| enzsub_graph | 4.389 | 0.104 | 6.074 | |
| enzsub_resources | 0.125 | 0.005 | 0.647 | |
| enzyme_substrate | 2.960 | 0.023 | 3.651 | |
| evex_download | 0.017 | 0.002 | 0.020 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 28.767 | 0.453 | 31.097 | |
| extra_attrs | 16.016 | 0.079 | 16.502 | |
| extra_attrs_to_cols | 25.290 | 0.100 | 26.069 | |
| filter_by_resource | 13.893 | 0.271 | 15.640 | |
| filter_extra_attrs | 51.958 | 0.333 | 60.975 | |
| filter_intercell | 9.654 | 0.722 | 18.949 | |
| filter_intercell_network | 0.036 | 0.002 | 0.079 | |
| find_all_paths | 12.878 | 0.267 | 24.305 | |
| from_evidences | 0.001 | 0.001 | 0.002 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.018 | 0.002 | 0.040 | |
| giant_component | 22.048 | 0.477 | 43.889 | |
| go_annot_download | 20.608 | 2.194 | 36.645 | |
| go_annot_slim | 0.001 | 0.001 | 0.001 | |
| go_ontology_download | 0.017 | 0.001 | 0.038 | |
| guide2pharma_download | 0.019 | 0.002 | 0.038 | |
| harmonizome_download | 0.017 | 0.002 | 0.047 | |
| has_extra_attrs | 16.286 | 0.151 | 24.450 | |
| hmdb_id_mapping_table | 0.018 | 0.001 | 0.021 | |
| hmdb_id_type | 0.004 | 0.001 | 0.007 | |
| hmdb_metabolite_fields | 0.001 | 0.002 | 0.002 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.002 | |
| hmdb_table | 0.018 | 0.002 | 0.021 | |
| homologene_download | 0.019 | 0.002 | 0.021 | |
| homologene_raw | 0.037 | 0.003 | 0.042 | |
| homologene_uniprot_orthology | 0.018 | 0.001 | 0.021 | |
| hpo_download | 3.569 | 0.384 | 4.208 | |
| htridb_download | 0.017 | 0.001 | 0.021 | |
| id_translation_resources | 0.001 | 0.001 | 0.001 | |
| id_types | 0.076 | 0.001 | 0.079 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0.000 | 0.000 | 0.002 | |
| interaction_datasets | 0.675 | 0.049 | 1.205 | |
| interaction_graph | 0.840 | 0.012 | 1.585 | |
| interaction_resources | 0.129 | 0.012 | 0.802 | |
| interaction_types | 0.086 | 0.006 | 0.113 | |
| intercell | 0.797 | 0.061 | 1.421 | |
| intercell_categories | 0.840 | 0.073 | 1.252 | |
| intercell_consensus_filter | 2.003 | 0.163 | 2.915 | |
| intercell_generic_categories | 0.082 | 0.004 | 0.090 | |
| intercell_network | 0.019 | 0.002 | 0.022 | |
| intercell_resources | 0.126 | 0.006 | 0.816 | |
| intercell_summary | 0.095 | 0.030 | 0.203 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.059 | 0.003 | 0.063 | |
| is_trembl | 0.054 | 0.003 | 0.060 | |
| is_uniprot | 0.019 | 0.001 | 0.021 | |
| kegg_info | 0.018 | 0.001 | 0.020 | |
| kegg_open | 0.017 | 0.001 | 0.019 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.018 | 0.002 | 0.020 | |
| kegg_pathway_list | 0.018 | 0.001 | 0.019 | |
| kegg_pathways_download | 0.001 | 0.001 | 0.002 | |
| kegg_picture | 0.116 | 0.012 | 8.052 | |
| kegg_process | 0.035 | 0.002 | 0.037 | |
| latin_name | 0.105 | 0.001 | 0.109 | |
| load_db | 0.195 | 0.008 | 0.212 | |
| ncbi_taxid | 0.107 | 0.001 | 0.119 | |
| nichenet_build_model | 0.000 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.020 | 0.002 | 0.022 | |
| nichenet_gr_network | 0.055 | 0.003 | 0.065 | |
| nichenet_gr_network_evex | 0.019 | 0.001 | 0.023 | |
| nichenet_gr_network_harmonizome | 0.019 | 0.001 | 0.023 | |
| nichenet_gr_network_htridb | 0.018 | 0.001 | 0.022 | |
| nichenet_gr_network_omnipath | 26.777 | 1.008 | 30.422 | |
| nichenet_gr_network_pathwaycommons | 0.018 | 0.001 | 0.020 | |
| nichenet_gr_network_regnetwork | 0.021 | 0.002 | 0.024 | |
| nichenet_gr_network_remap | 0.020 | 0.002 | 0.022 | |
| nichenet_gr_network_trrust | 0.017 | 0.001 | 0.061 | |
| nichenet_ligand_activities | 0.001 | 0.001 | 0.002 | |
| nichenet_ligand_target_links | 0.000 | 0.002 | 0.002 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.052 | 0.004 | 0.060 | |
| nichenet_lr_network_guide2pharma | 0.017 | 0.001 | 0.019 | |
| nichenet_lr_network_omnipath | 0.091 | 0.007 | 0.102 | |
| nichenet_lr_network_ramilowski | 0.018 | 0.001 | 0.021 | |
| nichenet_main | 0.001 | 0.001 | 0.002 | |
| nichenet_networks | 0.085 | 0.009 | 0.099 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.050 | 0.003 | 0.054 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.054 | 0.003 | 0.062 | |
| nichenet_signaling_network_cpdb | 0.018 | 0.001 | 0.020 | |
| nichenet_signaling_network_evex | 0.017 | 0.001 | 0.020 | |
| nichenet_signaling_network_harmonizome | 0.018 | 0.001 | 0.019 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 18.484 | 0.564 | 20.761 | |
| nichenet_signaling_network_pathwaycommons | 0.018 | 0.001 | 0.021 | |
| nichenet_signaling_network_vinayagam | 0.018 | 0.002 | 0.021 | |
| nichenet_test | 0.000 | 0.001 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.165 | 0.011 | 0.230 | |
| oma_code | 0.052 | 0.002 | 0.055 | |
| oma_organisms | 0.107 | 0.004 | 0.115 | |
| oma_pairwise | 0.017 | 0.002 | 0.020 | |
| oma_pairwise_genesymbols | 0.018 | 0.001 | 0.019 | |
| oma_pairwise_translated | 0.017 | 0.001 | 0.019 | |
| omnipath-interactions | 56.976 | 1.561 | 82.633 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.016 | 0.001 | 0.036 | |
| omnipath_cache_clean_db | 0.285 | 0.012 | 0.532 | |
| omnipath_cache_download_ready | 0.999 | 0.086 | 1.884 | |
| omnipath_cache_filter_versions | 0.179 | 0.019 | 0.231 | |
| omnipath_cache_get | 0.149 | 0.016 | 0.167 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.003 | |
| omnipath_cache_latest_or_new | 0.110 | 0.013 | 0.124 | |
| omnipath_cache_load | 0.915 | 0.036 | 1.775 | |
| omnipath_cache_move_in | 0.285 | 0.029 | 0.375 | |
| omnipath_cache_remove | 0.224 | 0.020 | 0.312 | |
| omnipath_cache_save | 0.258 | 0.024 | 0.438 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.140 | 0.014 | 0.174 | |
| omnipath_cache_update_status | 0.159 | 0.015 | 0.219 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.001 | 0.002 | |
| omnipath_for_cosmos | 17.176 | 0.377 | 40.536 | |
| omnipath_load_config | 0.000 | 0.001 | 0.001 | |
| omnipath_log | 0.000 | 0.001 | 0.000 | |
| omnipath_logfile | 0.003 | 0.001 | 0.013 | |
| omnipath_msg | 0.009 | 0.001 | 0.022 | |
| omnipath_query | 9.475 | 0.060 | 18.446 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.011 | |
| omnipath_save_config | 0.000 | 0.001 | 0.001 | |
| omnipath_set_cachedir | 0.050 | 0.004 | 0.102 | |
| omnipath_set_console_loglevel | 0.007 | 0.001 | 0.007 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.008 | |
| omnipath_set_loglevel | 0.004 | 0.001 | 0.004 | |
| omnipath_show_db | 0.178 | 0.002 | 0.367 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0.001 | 0.001 | 0.000 | |
| ontology_ensure_id | 0.001 | 0.001 | 0.002 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.003 | |
| ontology_name_id | 0.001 | 0.001 | 0.003 | |
| organism_for | 0.080 | 0.002 | 0.163 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.012 | |
| pivot_annotations | 16.574 | 1.383 | 26.976 | |
| preppi_download | 0.001 | 0.001 | 0.002 | |
| preppi_filter | 0.002 | 0.001 | 0.002 | |
| print_bma_motif_es | 0.369 | 0.036 | 1.203 | |
| print_bma_motif_vs | 0.224 | 0.006 | 0.718 | |
| print_interactions | 12.895 | 0.308 | 15.658 | |
| print_path_es | 0.906 | 0.044 | 1.981 | |
| print_path_vs | 4.630 | 0.095 | 6.586 | |
| pubmed_open | 9.507 | 0.130 | 10.040 | |
| query_info | 0.162 | 0.015 | 3.096 | |
| ramilowski_download | 0.001 | 0.001 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.001 | 0.002 | |
| ramp_id_type | 0.004 | 0.001 | 0.005 | |
| ramp_sqlite | 0.001 | 0.000 | 0.002 | |
| ramp_table | 0.001 | 0.001 | 0.002 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.001 | 0.002 | |
| regnetwork_download | 0.001 | 0.001 | 0.003 | |
| relations_list_to_table | 0.166 | 0.009 | 0.299 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.001 | |
| relations_table_to_list | 0.140 | 0.006 | 0.190 | |
| remap_dorothea_download | 0.001 | 0.001 | 0.002 | |
| remap_filtered | 0.000 | 0.000 | 0.001 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.002 | |
| resource_info | 0.293 | 0.126 | 0.984 | |
| resources | 0.112 | 0.006 | 0.782 | |
| resources_colname | 0.907 | 0.088 | 1.760 | |
| resources_in | 9.198 | 0.038 | 9.716 | |
| show_network | 0.000 | 0.000 | 0.001 | |
| signed_ptms | 11.856 | 0.053 | 13.083 | |
| simplify_intercell_network | 0.001 | 0.001 | 0.002 | |
| static_table | 9.687 | 0.728 | 14.156 | |
| static_tables | 0.091 | 0.001 | 0.203 | |
| stitch_actions | 0.001 | 0.001 | 0.003 | |
| stitch_links | 0.001 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.001 | 0.002 | |
| stitch_remove_prefixes | 0.012 | 0.001 | 0.013 | |
| swap_relations | 0.143 | 0.005 | 0.169 | |
| swissprots_only | 0.059 | 0.000 | 0.062 | |
| tfcensus_download | 0.301 | 0.021 | 0.480 | |
| translate_ids | 1.839 | 0.132 | 20.135 | |
| translate_ids_multi | 13.246 | 0.215 | 28.959 | |
| trembls_only | 0.058 | 0.000 | 0.060 | |
| trrust_download | 0.001 | 0.001 | 0.002 | |
| uniprot_full_id_mapping_table | 1.470 | 0.141 | 89.783 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.002 | |
| uniprot_id_type | 0.004 | 0.001 | 0.005 | |
| uniprot_idmapping_id_types | 0.319 | 0.017 | 0.823 | |
| unique_intercell_network | 0.001 | 0.001 | 0.002 | |
| unnest_evidences | 0.000 | 0.000 | 0.001 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.004 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.002 | 0.002 | 0.003 | |
| with_extra_attrs | 20.787 | 0.271 | 21.814 | |
| with_references | 0.743 | 0.043 | 1.951 | |
| zenodo_download | 0.002 | 0.001 | 0.004 | |