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This page was generated on 2025-03-10 12:09 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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Package 1456/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.14.0  (landing page)
Denes Turei
Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

CHECK results for OmnipathR on merida1

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.

raw results


Summary

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: 2025-03-07 07:28:20 -0500 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 07:51:46 -0500 (Fri, 07 Mar 2025)
EllapsedTime: 1406.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:06] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 07:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 07:29:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:07] [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
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 07:29:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:29:37] [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                101.989  0.338 105.293
curated_ligrec_stats                  58.510  1.645 127.534
omnipath-interactions                 53.617  1.498 134.331
filter_extra_attrs                    51.938  0.209  54.621
extra_attr_values                     28.920  0.407  34.771
nichenet_gr_network_omnipath          26.824  1.116  55.829
extra_attrs_to_cols                   25.267  0.112  26.227
giant_component                       21.564  0.454  26.476
with_extra_attrs                      21.019  0.297  23.198
nichenet_signaling_network_omnipath   18.711  0.578  41.551
go_annot_download                     17.311  1.397  23.663
pivot_annotations                     17.078  1.309  32.717
omnipath_for_cosmos                   17.425  0.364  64.515
has_extra_attrs                       16.003  0.109  16.532
extra_attrs                           15.878  0.078  16.381
translate_ids_multi                   13.644  0.266  38.332
filter_by_resource                    13.593  0.197  17.313
print_interactions                    12.598  0.231  19.006
find_all_paths                        12.512  0.214  13.030
signed_ptms                           11.428  0.053  12.642
static_table                           9.431  0.738  11.106
curated_ligand_receptor_interactions   9.385  0.359  20.172
filter_intercell                       9.011  0.628  14.550
omnipath_query                         9.407  0.072  10.597
pubmed_open                            9.293  0.091   9.945
resources_in                           8.914  0.044   9.390
print_path_vs                          4.699  0.184   7.336
enzsub_graph                           4.589  0.101   6.821
intercell_consensus_filter             1.981  0.124   5.406
translate_ids                          1.839  0.100  22.664
ensembl_id_mapping_table               1.776  0.144  28.739
biomart_query                          1.446  0.158  17.076
all_uniprots                           1.451  0.143  25.032
uniprot_full_id_mapping_table          1.125  0.082  27.859
* 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.

Installation output

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
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-06 16:17:23] [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).
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:23] [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).
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:23] [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).
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:23] [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).
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:23] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-06 16:17:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:17:28] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

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)
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Contains 21 files.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:50:21] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 21.274   1.564  59.819

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0010.002
all_uniprot_acs0.0360.0060.042
all_uniprots 1.451 0.14325.032
ancestors0.0190.0020.021
annotated_network1.3700.0944.136
annotation_categories101.989 0.338105.293
annotation_resources0.1260.0080.791
annotations0.4860.0271.507
biomart_query 1.446 0.15817.076
bioplex10.0180.0020.020
bioplex20.0180.0020.020
bioplex30.0180.0010.019
bioplex_all0.0180.0020.020
bioplex_hct116_10.0180.0020.019
bma_motif_es0.6600.0421.820
bma_motif_vs0.3510.0101.023
chalmers_gem0.0180.0010.060
chalmers_gem_id_mapping_table0.0190.0010.020
chalmers_gem_id_type0.0030.0010.004
chalmers_gem_metabolites0.0180.0010.020
chalmers_gem_network0.0180.0010.021
chalmers_gem_raw0.0190.0020.022
chalmers_gem_reactions0.0190.0010.022
common_name0.0530.0010.056
complex_genes0.8180.0422.170
complex_resources0.1250.0040.589
complexes0.3060.0080.781
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0180.0010.020
cosmos_pkn0.0000.0010.001
curated_ligand_receptor_interactions 9.385 0.35920.172
curated_ligrec_stats 58.510 1.645127.534
database_summary2.6690.0513.708
descendants0.0180.0010.021
ensembl_dataset0.0180.0010.021
ensembl_id_mapping_table 1.776 0.14428.739
ensembl_id_type0.0040.0000.004
ensembl_name0.1090.0020.113
ensembl_organisms0.3070.0050.318
ensembl_organisms_raw0.2580.0030.269
ensembl_orthology0.0000.0010.002
enzsub_graph4.5890.1016.821
enzsub_resources0.1190.0050.587
enzyme_substrate2.3910.0163.120
evex_download0.0170.0020.020
evidences0.0000.0010.001
extra_attr_values28.920 0.40734.771
extra_attrs15.878 0.07816.381
extra_attrs_to_cols25.267 0.11226.227
filter_by_resource13.593 0.19717.313
filter_extra_attrs51.938 0.20954.621
filter_intercell 9.011 0.62814.550
filter_intercell_network0.0360.0020.039
find_all_paths12.512 0.21413.030
from_evidences0.0000.0010.001
get_db0.0010.0010.001
get_ontology_db0.0180.0030.021
giant_component21.564 0.45426.476
go_annot_download17.311 1.39723.663
go_annot_slim0.0000.0010.002
go_ontology_download0.0180.0020.020
guide2pharma_download0.0200.0030.023
harmonizome_download0.0190.0020.020
has_extra_attrs16.003 0.10916.532
hmdb_id_mapping_table0.0180.0020.020
hmdb_id_type0.0040.0000.005
hmdb_metabolite_fields0.0000.0020.005
hmdb_protein_fields0.0010.0010.001
hmdb_table0.0180.0010.022
homologene_download0.0180.0020.020
homologene_raw0.0350.0030.038
homologene_uniprot_orthology0.0180.0020.021
hpo_download3.5630.3964.095
htridb_download0.0180.0020.022
id_translation_resources0.0010.0000.001
id_types0.0760.0020.082
inbiomap_download0.0010.0010.001
inbiomap_raw0.0000.0000.001
interaction_datasets0.6600.0431.025
interaction_graph0.7790.0141.966
interaction_resources0.1240.0120.655
interaction_types0.0840.0040.172
intercell0.7630.0572.039
intercell_categories0.6730.0691.833
intercell_consensus_filter1.9810.1245.406
intercell_generic_categories0.0830.0040.176
intercell_network0.0200.0010.051
intercell_resources0.1230.0060.658
intercell_summary0.1000.0310.270
is_ontology_id0.0000.0000.001
is_swissprot0.0620.0030.124
is_trembl0.0630.0030.138
is_uniprot0.0240.0020.055
kegg_info0.0190.0010.040
kegg_open0.0190.0010.039
kegg_pathway_annotations0.0000.0010.001
kegg_pathway_download0.0180.0010.040
kegg_pathway_list0.0180.0020.042
kegg_pathways_download000
kegg_picture0.1600.0161.918
kegg_process0.0340.0030.036
latin_name0.1020.0010.194
load_db0.1420.0050.299
ncbi_taxid0.1030.0020.203
nichenet_build_model0.0010.0010.001
nichenet_expression_data0.0180.0020.039
nichenet_gr_network0.0510.0030.145
nichenet_gr_network_evex0.0170.0010.050
nichenet_gr_network_harmonizome0.0190.0020.040
nichenet_gr_network_htridb0.0170.0010.037
nichenet_gr_network_omnipath26.824 1.11655.829
nichenet_gr_network_pathwaycommons0.0170.0010.032
nichenet_gr_network_regnetwork0.0170.0020.040
nichenet_gr_network_remap0.0180.0010.040
nichenet_gr_network_trrust0.0180.0020.041
nichenet_ligand_activities0.0000.0010.002
nichenet_ligand_target_links0.0010.0020.013
nichenet_ligand_target_matrix0.0000.0010.001
nichenet_lr_network0.1990.0100.422
nichenet_lr_network_guide2pharma0.0220.0020.053
nichenet_lr_network_omnipath0.0670.0050.140
nichenet_lr_network_ramilowski0.0230.0020.045
nichenet_main0.0010.0010.002
nichenet_networks0.1160.0100.249
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0650.0040.140
nichenet_results_dir0.0010.0000.000
nichenet_signaling_network0.0710.0060.156
nichenet_signaling_network_cpdb0.0220.0010.043
nichenet_signaling_network_evex0.0200.0020.042
nichenet_signaling_network_harmonizome0.0190.0010.039
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath18.711 0.57841.551
nichenet_signaling_network_pathwaycommons0.0180.0020.086
nichenet_signaling_network_vinayagam0.0180.0010.079
nichenet_test0.0000.0010.000
nichenet_workarounds0.0000.0010.001
obo_parser0.1690.0100.587
oma_code0.0540.0010.106
oma_organisms0.0950.0030.216
oma_pairwise0.0680.0030.150
oma_pairwise_genesymbols0.0180.0010.070
oma_pairwise_translated0.0180.0020.076
omnipath-interactions 53.617 1.498134.331
omnipath_cache_autoclean0.0010.0010.000
omnipath_cache_clean0.0150.0010.018
omnipath_cache_clean_db0.2070.0140.228
omnipath_cache_download_ready0.9500.0681.179
omnipath_cache_filter_versions0.2290.0190.293
omnipath_cache_get0.1590.0170.410
omnipath_cache_key0.0020.0010.003
omnipath_cache_latest_or_new0.1240.0130.298
omnipath_cache_load0.9490.0402.549
omnipath_cache_move_in0.2940.0310.640
omnipath_cache_remove0.2360.0230.571
omnipath_cache_save0.2800.0260.636
omnipath_cache_search0.0010.0000.002
omnipath_cache_set_ext0.1440.0160.320
omnipath_cache_update_status0.1700.0170.440
omnipath_cache_wipe000
omnipath_config_path0.0010.0000.012
omnipath_for_cosmos17.425 0.36464.515
omnipath_load_config0.0000.0010.011
omnipath_log0.0000.0010.001
omnipath_logfile0.0030.0010.003
omnipath_msg0.0100.0020.021
omnipath_query 9.407 0.07210.597
omnipath_reset_config0.0010.0010.001
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0540.0050.064
omnipath_set_console_loglevel0.0080.0010.009
omnipath_set_logfile_loglevel0.0070.0010.008
omnipath_set_loglevel0.0040.0010.006
omnipath_show_db0.1110.0020.167
omnipath_unlock_cache_db0.0010.0000.001
only_from0.0000.0010.001
ontology_ensure_id0.0010.0000.002
ontology_ensure_name0.0010.0010.002
ontology_name_id0.0020.0010.003
organism_for0.0710.0030.076
pathwaycommons_download0.0010.0010.002
pivot_annotations17.078 1.30932.717
preppi_download0.0010.0010.002
preppi_filter0.0020.0010.003
print_bma_motif_es0.3270.0321.105
print_bma_motif_vs0.2590.0060.834
print_interactions12.598 0.23119.006
print_path_es0.8560.0451.919
print_path_vs4.6990.1847.336
pubmed_open9.2930.0919.945
query_info0.1630.0153.226
ramilowski_download0.0010.0010.003
ramp_id_mapping_table0.0010.0010.001
ramp_id_type0.0040.0010.007
ramp_sqlite0.0010.0010.001
ramp_table0.0010.0010.001
ramp_tables0.0010.0000.001
regnetwork_directions0.0010.0010.005
regnetwork_download0.0020.0010.002
relations_list_to_table0.1550.0070.365
relations_table_to_graph0.0010.0000.001
relations_table_to_list0.1360.0050.173
remap_dorothea_download0.0010.0010.003
remap_filtered0.0000.0010.001
remap_tf_target_download0.0010.0010.001
resource_info0.2980.1340.962
resources0.1100.0100.594
resources_colname0.9060.0682.563
resources_in8.9140.0449.390
show_network0.0000.0010.000
signed_ptms11.428 0.05312.642
simplify_intercell_network0.0010.0000.002
static_table 9.431 0.73811.106
static_tables0.0920.0010.190
stitch_actions0.0010.0010.001
stitch_links0.0010.0000.002
stitch_network0.0010.0010.002
stitch_remove_prefixes0.0120.0010.013
swap_relations0.1430.0050.151
swissprots_only0.1300.0010.134
tfcensus_download0.2870.0200.438
translate_ids 1.839 0.10022.664
translate_ids_multi13.644 0.26638.332
trembls_only0.0510.0010.052
trrust_download0.0010.0010.002
uniprot_full_id_mapping_table 1.125 0.08227.859
uniprot_genesymbol_cleanup0.0010.0000.001
uniprot_id_mapping_table0.0010.0010.002
uniprot_id_type0.0040.0010.005
uniprot_idmapping_id_types0.3110.0170.824
unique_intercell_network0.0020.0010.003
unnest_evidences0.0000.0000.001
uploadlists_id_type0.0040.0010.005
vinayagam_download0.0010.0010.002
walk_ontology_tree0.0020.0010.004
with_extra_attrs21.019 0.29723.198
with_references0.7510.0441.798
zenodo_download0.0020.0010.004