Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-02-01 11:43 -0500 (Sat, 01 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4431
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1454/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.15.0  (landing page)
Denes Turei
Snapshot Date: 2025-01-31 13:40 -0500 (Fri, 31 Jan 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: bc4d2dd
git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES

CHECK results for OmnipathR on lconway

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: 3.15.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
StartedAt: 2025-01-31 21:59:23 -0500 (Fri, 31 Jan 2025)
EndedAt: 2025-01-31 22:13:16 -0500 (Fri, 31 Jan 2025)
EllapsedTime: 832.7 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_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS 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 ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 21:59:52] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 22:00:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:00:09] [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                60.154  0.159  61.803
curated_ligrec_stats                 29.231  6.179 112.718
omnipath-interactions                26.711  1.257  58.799
filter_extra_attrs                   17.369  0.094  18.059
nichenet_gr_network_omnipath         15.616  0.795  22.629
go_annot_download                    12.540  1.017  24.211
nichenet_signaling_network_omnipath  12.471  0.568  19.398
extra_attrs_to_cols                  11.975  0.233  12.291
with_extra_attrs                     10.842  0.318  13.938
giant_component                      10.580  0.553  17.362
pivot_annotations                    10.126  0.903  19.864
extra_attr_values                    10.256  0.218  13.150
omnipath_for_cosmos                   7.618  0.362  23.294
filter_intercell                      7.010  0.596  16.707
filter_by_resource                    7.371  0.222   9.877
static_table                          6.384  0.527   7.482
translate_ids_multi                   5.891  0.217  23.290
extra_attrs                           5.959  0.030   6.000
find_all_paths                        5.518  0.249  10.094
print_interactions                    5.479  0.225   9.648
has_extra_attrs                       5.298  0.136   7.309
signed_ptms                           4.791  0.035   5.430
curated_ligand_receptor_interactions  4.490  0.267  13.900
print_path_vs                         2.146  0.143   5.054
database_summary                      1.375  0.361   5.459
ensembl_id_mapping_table              1.242  0.479  14.639
uniprot_full_id_mapping_table         1.085  0.130  22.099
translate_ids                         1.087  0.077  18.473
all_uniprots                          0.812  0.092  22.464
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.15.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:18] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:22] [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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
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)
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Contains 21 files.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 22:12:21] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 10.963   1.077  39.510

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.001
all_uniprot_acs0.0170.0030.020
all_uniprots 0.812 0.09222.464
ancestors0.0100.0010.012
annotated_network0.7460.0674.208
annotation_categories60.154 0.15961.803
annotation_resources0.0600.0040.603
annotations0.2480.0181.095
biomart_query0.9690.1353.637
bioplex10.0100.0010.010
bioplex20.0070.0010.007
bioplex30.0090.0010.011
bioplex_all0.0390.0020.040
bioplex_hct116_10.0070.0000.007
bma_motif_es0.3500.0331.183
bma_motif_vs0.2010.0060.795
chalmers_gem0.0080.0000.008
chalmers_gem_id_mapping_table0.0090.0010.010
chalmers_gem_id_type0.0020.0000.003
chalmers_gem_metabolites0.0090.0000.009
chalmers_gem_network0.0120.0000.012
chalmers_gem_raw0.0090.0000.009
chalmers_gem_reactions0.0080.0010.010
common_name0.0250.0000.026
complex_genes0.4760.0242.235
complex_resources0.0620.0030.598
complexes0.1680.0060.709
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0100.0000.011
cosmos_pkn000
curated_ligand_receptor_interactions 4.490 0.26713.900
curated_ligrec_stats 29.231 6.179112.718
database_summary1.3750.3615.459
descendants0.0110.0020.013
ensembl_dataset0.0110.0010.011
ensembl_id_mapping_table 1.242 0.47914.639
ensembl_id_type0.0030.0010.003
ensembl_name0.0580.0010.059
ensembl_organisms0.2020.0060.210
ensembl_organisms_raw0.0950.0020.097
ensembl_orthology0.0000.0000.001
enzsub_graph2.3600.0774.532
enzsub_resources0.0610.0040.633
enzyme_substrate1.0860.0711.892
evex_download0.0110.0030.022
evidences000
extra_attr_values10.256 0.21813.150
extra_attrs5.9590.0306.000
extra_attrs_to_cols11.975 0.23312.291
filter_by_resource7.3710.2229.877
filter_extra_attrs17.369 0.09418.059
filter_intercell 7.010 0.59616.707
filter_intercell_network0.0140.0020.023
find_all_paths 5.518 0.24910.094
from_evidences0.0000.0010.002
get_db0.0000.0010.000
get_ontology_db0.0090.0010.012
giant_component10.580 0.55317.362
go_annot_download12.540 1.01724.211
go_annot_slim0.0000.0010.000
go_ontology_download0.0060.0010.007
guide2pharma_download0.0060.0010.006
harmonizome_download0.0050.0010.007
has_extra_attrs5.2980.1367.309
hmdb_id_mapping_table0.0110.0010.012
hmdb_id_type0.0020.0010.003
hmdb_metabolite_fields0.0000.0010.001
hmdb_protein_fields0.0000.0010.001
hmdb_table0.0110.0010.012
homologene_download0.0100.0010.010
homologene_raw0.0180.0010.019
homologene_uniprot_orthology0.0110.0010.012
hpo_download1.9660.4182.493
htridb_download0.0080.0010.009
id_translation_resources0.0000.0010.001
id_types0.0400.0010.040
inbiomap_download000
inbiomap_raw000
interaction_datasets0.3740.0220.764
interaction_graph0.5330.0151.304
interaction_resources0.0770.0070.678
interaction_types0.0520.0030.055
intercell0.4950.0481.348
intercell_categories0.4230.0380.914
intercell_consensus_filter1.4750.1143.870
intercell_generic_categories0.0590.0030.111
intercell_network0.0140.0010.022
intercell_resources0.0770.0030.628
intercell_summary0.0600.0160.076
is_ontology_id0.0000.0010.000
is_swissprot0.0340.0020.037
is_trembl0.0340.0020.047
is_uniprot0.0130.0010.017
kegg_info0.0120.0000.025
kegg_open0.0110.0010.018
kegg_pathway_annotations0.0000.0010.000
kegg_pathway_download0.0120.0010.020
kegg_pathway_list0.0110.0010.025
kegg_pathways_download0.0000.0000.001
kegg_picture0.1310.0194.105
kegg_process0.0210.0020.023
latin_name0.0680.0000.070
load_db0.0930.0020.110
ncbi_taxid0.0780.0010.133
nichenet_build_model000
nichenet_expression_data0.0130.0020.026
nichenet_gr_network0.0390.0030.064
nichenet_gr_network_evex0.0130.0010.026
nichenet_gr_network_harmonizome0.0140.0010.027
nichenet_gr_network_htridb0.0130.0010.023
nichenet_gr_network_omnipath15.616 0.79522.629
nichenet_gr_network_pathwaycommons0.0080.0000.008
nichenet_gr_network_regnetwork0.0070.0000.009
nichenet_gr_network_remap0.0090.0010.011
nichenet_gr_network_trrust0.0100.0010.011
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0270.0020.030
nichenet_lr_network_guide2pharma0.0090.0010.009
nichenet_lr_network_omnipath0.0280.0020.030
nichenet_lr_network_ramilowski0.0080.0010.009
nichenet_main0.0000.0000.001
nichenet_networks0.0490.0050.055
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0250.0020.027
nichenet_results_dir000
nichenet_signaling_network0.0260.0020.028
nichenet_signaling_network_cpdb0.0090.0010.010
nichenet_signaling_network_evex0.0090.0010.009
nichenet_signaling_network_harmonizome0.0100.0000.012
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath12.471 0.56819.398
nichenet_signaling_network_pathwaycommons0.0110.0010.012
nichenet_signaling_network_vinayagam0.0110.0000.011
nichenet_test000
nichenet_workarounds000
obo_parser0.1030.0070.176
oma_code0.0340.0000.035
oma_organisms0.0970.0030.099
oma_pairwise0.0130.0020.014
oma_pairwise_genesymbols0.0140.0010.015
oma_pairwise_translated0.0120.0010.013
omnipath-interactions26.711 1.25758.799
omnipath_cache_autoclean000
omnipath_cache_clean0.0060.0010.008
omnipath_cache_clean_db0.1010.0120.162
omnipath_cache_download_ready0.5120.0430.654
omnipath_cache_filter_versions0.1060.0130.140
omnipath_cache_get0.0960.0110.109
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.0680.0080.077
omnipath_cache_load0.5980.0313.057
omnipath_cache_move_in0.1660.0230.199
omnipath_cache_remove0.1170.0140.137
omnipath_cache_save0.1600.0170.196
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.0930.0110.111
omnipath_cache_update_status0.1230.0120.138
omnipath_cache_wipe000
omnipath_config_path0.0000.0010.001
omnipath_for_cosmos 7.618 0.36223.294
omnipath_load_config0.0010.0000.000
omnipath_log000
omnipath_logfile0.0010.0000.002
omnipath_msg0.0040.0000.005
omnipath_query3.8530.0533.939
omnipath_reset_config0.0010.0000.000
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0280.0030.031
omnipath_set_console_loglevel0.0030.0000.003
omnipath_set_logfile_loglevel0.0020.0000.003
omnipath_set_loglevel0.0010.0000.001
omnipath_show_db0.0610.0010.062
omnipath_unlock_cache_db0.0000.0000.001
only_from0.0000.0000.001
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0000.0010.001
ontology_name_id0.0010.0010.001
organism_for0.0470.0010.048
pathwaycommons_download0.0010.0010.001
pivot_annotations10.126 0.90319.864
preppi_download000
preppi_filter0.0000.0000.001
print_bma_motif_es0.1990.0371.034
print_bma_motif_vs0.1040.0050.728
print_interactions5.4790.2259.648
print_path_es0.4860.0352.273
print_path_vs2.1460.1435.054
pubmed_open3.9040.0544.008
query_info0.0690.0070.315
ramilowski_download0.0000.0010.001
ramp_id_mapping_table0.0000.0010.001
ramp_id_type0.0010.0000.002
ramp_sqlite0.0000.0000.001
ramp_table0.0010.0000.001
ramp_tables000
regnetwork_directions0.0000.0010.001
regnetwork_download0.0010.0010.001
relations_list_to_table0.0790.0053.164
relations_table_to_graph0.0010.0000.000
relations_table_to_list0.0740.0030.090
remap_dorothea_download0.0010.0000.001
remap_filtered0.0000.0000.001
remap_tf_target_download000
resource_info0.1360.0730.825
resources0.0490.0040.782
resources_colname0.5960.0442.427
resources_in3.3510.0223.400
show_network000
signed_ptms4.7910.0355.430
simplify_intercell_network0.0010.0000.001
static_table6.3840.5277.482
static_tables0.0600.0010.067
stitch_actions0.0000.0000.001
stitch_links0.0010.0000.001
stitch_network0.0010.0000.001
stitch_remove_prefixes0.0090.0000.009
swap_relations0.1690.0110.208
swissprots_only0.0410.0000.041
tfcensus_download0.1690.0160.419
translate_ids 1.087 0.07718.473
translate_ids_multi 5.891 0.21723.290
trembls_only0.0270.0000.027
trrust_download0.0010.0000.001
uniprot_full_id_mapping_table 1.085 0.13022.099
uniprot_genesymbol_cleanup0.0010.0000.001
uniprot_id_mapping_table0.0010.0000.001
uniprot_id_type0.0030.0000.003
uniprot_idmapping_id_types0.1620.0100.882
unique_intercell_network0.0010.0000.000
unnest_evidences000
uploadlists_id_type0.0010.0000.002
vinayagam_download000
walk_ontology_tree0.0000.0000.001
with_extra_attrs10.842 0.31813.938
with_references0.4400.0382.020
zenodo_download0.0010.0010.001