Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:35 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1425/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.8.2  (landing page)
Denes Turei
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_17
git_last_commit: b12b9bf
git_last_commit_date: 2023-09-15 08:58:47 -0400 (Fri, 15 Sep 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for OmnipathR on nebbiolo1


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: 3.8.2
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.8.2.tar.gz
StartedAt: 2023-10-15 23:26:17 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 23:55:15 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 1737.7 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.8.2’
* 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 R 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 23:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:34] [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
[2023-10-15 23:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:26:43] [TRACE]   [OmnipathR] Cache locked: FALSE
uniprot_idmapping_id_types: no visible binding for global variable
  ‘groups’
uniprot_idmapping_id_types: no visible binding for global variable
  ‘items’
Undefined global functions or variables:
  groups items
* 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
collectri                              92.628  0.712  96.414
dorothea                               64.003  1.240  69.669
annotation_categories                  65.140  0.072  66.715
curated_ligrec_stats                   42.446  2.237 130.656
filter_extra_attrs                     35.974  0.128  37.495
nichenet_gr_network_omnipath           21.242  0.755  42.666
pivot_annotations                      17.466  1.331  40.047
giant_component                        17.718  0.233  31.554
go_annot_download                      14.326  1.976  18.580
extra_attrs_to_cols                    16.090  0.075  16.614
nichenet_signaling_network_omnipath    15.523  0.287  27.795
extra_attr_values                      12.661  0.423  18.438
has_extra_attrs                        10.839  0.453  19.333
print_interactions                     10.297  0.653  19.885
filter_by_resource                     10.259  0.107  15.537
extra_attrs                            10.098  0.175  10.281
filter_intercell                        9.218  0.231  14.496
find_all_paths                          8.666  0.070   9.321
curated_ligand_receptor_interactions    8.125  0.587  25.491
pubmed_open                             7.635  0.452  10.225
with_extra_attrs                        7.094  0.157   9.420
get_signed_ptms                         6.665  0.011   7.371
omnipath                                6.224  0.022   9.140
database_summary                        2.350  2.065   7.214
import_transcriptional_interactions     2.526  1.783  12.811
intercell_consensus_filter              2.530  0.511   7.406
enzsub_graph                            2.976  0.061   6.041
print_path_vs                           2.564  0.140   5.963
import_tf_target_interactions           1.269  0.997  19.546
import_omnipath_enzsub                  2.123  0.141   7.836
get_complex_genes                       1.987  0.031   5.276
import_pathwayextra_interactions        1.764  0.192   7.349
import_mirnatarget_interactions         1.643  0.159   7.162
import_ligrecextra_interactions         1.354  0.115   5.535
omnipath_cache_load                     1.352  0.101   6.644
ensembl_id_mapping_table                1.333  0.084  21.344
import_post_translational_interactions  1.108  0.283   6.604
biomart_query                           1.197  0.064  10.677
import_omnipath_complexes               1.121  0.061   6.256
kegg_picture                            0.343  0.065   6.981
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Contains 6 files.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:10] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-10-15 15:30:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:30:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 15:30:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:30:12] [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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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
> #  2018-2023
> #  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)
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Contains 16 files.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 23:43:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 23:43:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 23:43:34] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 20.910   1.241  63.840

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0250.0000.025
all_uniprots0.010.000.01
ancestors0.010.000.01
annotated_network1.2080.0724.933
annotation_categories65.140 0.07266.715
biomart_query 1.197 0.06410.677
bioplex10.0350.0000.034
bioplex20.0100.0000.009
bioplex30.0090.0000.010
bioplex_all0.0090.0000.010
bioplex_hct116_10.0100.0000.009
bma_motif_es0.4230.0241.482
bma_motif_vs0.2840.0000.949
collectri92.628 0.71296.414
common_name0.0660.0000.066
consensuspathdb_download000
consensuspathdb_raw_table0.0230.0000.024
curated_ligand_receptor_interactions 8.125 0.58725.491
curated_ligrec_stats 42.446 2.237130.656
database_summary2.3502.0657.214
descendants0.0200.0040.024
dorothea64.003 1.24069.669
ensembl_dataset0.0230.0040.027
ensembl_id_mapping_table 1.333 0.08421.344
ensembl_id_type0.0090.0000.009
ensembl_name0.1080.0000.108
ensembl_organisms0.2620.0080.270
ensembl_organisms_raw0.2470.0000.249
ensembl_orthology0.0000.0000.001
enzsub_graph2.9760.0616.041
evex_download0.0260.0030.030
evidences0.0010.0010.000
extra_attr_values12.661 0.42318.438
extra_attrs10.098 0.17510.281
extra_attrs_to_cols16.090 0.07516.614
filter_by_resource10.259 0.10715.537
filter_extra_attrs35.974 0.12837.495
filter_intercell 9.218 0.23114.496
filter_intercell_network0.0380.0040.042
find_all_paths8.6660.0709.321
from_evidences0.0010.0000.000
get_annotation_resources0.3030.0041.163
get_complex_genes1.9870.0315.276
get_complex_resources0.2520.0001.424
get_db0.0010.0000.001
get_enzsub_resources0.2440.0040.993
get_interaction_resources0.2510.0001.087
get_intercell_categories1.1010.0281.445
get_intercell_generic_categories0.0290.0080.037
get_intercell_resources0.2030.0031.123
get_ontology_db0.0190.0000.019
get_resources0.2100.0080.939
get_signed_ptms6.6650.0117.371
giant_component17.718 0.23331.554
go_annot_download14.326 1.97618.580
go_annot_slim000
go_ontology_download0.0250.0000.025
guide2pharma_download0.0290.0080.037
harmonizome_download0.0220.0080.030
has_extra_attrs10.839 0.45319.333
homologene_download0.0220.0000.022
homologene_raw0.0370.0080.046
homologene_uniprot_orthology0.0220.0000.022
homology_translate000
hpo_download2.5570.3664.428
htridb_download0.0080.0040.012
import_all_interactions0.9060.1162.934
import_intercell_network0.0110.0000.011
import_kinaseextra_interactions1.3010.1254.175
import_ligrecextra_interactions1.3540.1155.535
import_lncrna_mrna_interactions1.0180.0783.657
import_mirnatarget_interactions1.6430.1597.162
import_omnipath_annotations1.0430.1334.887
import_omnipath_complexes1.1210.0616.256
import_omnipath_enzsub2.1230.1417.836
import_omnipath_interactions0.5450.0242.103
import_omnipath_intercell0.9660.1353.339
import_pathwayextra_interactions1.7640.1927.349
import_post_translational_interactions1.1080.2836.604
import_small_molecule_protein_interactions0.4600.0561.102
import_tf_mirna_interactions0.7910.0773.296
import_tf_target_interactions 1.269 0.99719.546
import_transcriptional_interactions 2.526 1.78312.811
inbiomap_download000
inbiomap_raw000
interaction_datasets0.6260.0551.606
interaction_graph0.5810.0081.300
interaction_types0.0430.0030.047
intercell_categories0.0760.0090.085
intercell_consensus_filter2.5300.5117.406
is_ontology_id0.0000.0000.001
is_swissprot0.1060.0130.237
is_trembl0.1080.0240.275
is_uniprot0.0410.0040.112
kegg_info0.0350.0200.141
kegg_open0.0360.0000.094
kegg_pathway_annotations0.0010.0000.000
kegg_pathway_download0.0360.0000.088
kegg_pathway_list0.0250.0080.082
kegg_pathways_download0.0000.0000.001
kegg_picture0.3430.0656.981
kegg_process0.0540.0160.201
latin_name0.1560.0290.531
load_db0.2220.0280.498
ncbi_taxid0.2590.0480.475
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0250.0120.081
nichenet_gr_network0.0780.0260.196
nichenet_gr_network_evex0.0280.0040.065
nichenet_gr_network_harmonizome0.0330.0000.065
nichenet_gr_network_htridb0.0300.0000.058
nichenet_gr_network_omnipath21.242 0.75542.666
nichenet_gr_network_pathwaycommons0.0310.0000.062
nichenet_gr_network_regnetwork0.1300.0000.258
nichenet_gr_network_remap0.0240.0040.060
nichenet_gr_network_trrust0.0290.0000.061
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0830.0000.168
nichenet_lr_network_guide2pharma0.0240.0040.060
nichenet_lr_network_omnipath0.0650.0040.069
nichenet_lr_network_ramilowski0.0240.0040.028
nichenet_main0.0010.0000.001
nichenet_networks0.1390.0120.300
nichenet_optimization000
nichenet_remove_orphan_ligands0.0740.0120.134
nichenet_results_dir0.0000.0010.000
nichenet_signaling_network0.0630.0100.073
nichenet_signaling_network_cpdb0.0220.0000.022
nichenet_signaling_network_evex0.0230.0000.039
nichenet_signaling_network_harmonizome0.0300.0000.062
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath15.523 0.28727.795
nichenet_signaling_network_pathwaycommons0.0370.0000.046
nichenet_signaling_network_vinayagam0.0340.0000.034
nichenet_test000
nichenet_workarounds000
obo_parser0.2970.0240.905
omnipath6.2240.0229.140
omnipath_cache_autoclean000
omnipath_cache_clean0.0120.0010.013
omnipath_cache_clean_db0.1620.0080.259
omnipath_cache_download_ready1.1010.0881.726
omnipath_cache_filter_versions0.2560.0160.387
omnipath_cache_get0.2210.0160.237
omnipath_cache_key0.0000.0030.003
omnipath_cache_latest_or_new0.1850.0080.341
omnipath_cache_load1.3520.1016.644
omnipath_cache_move_in0.4730.0531.250
omnipath_cache_remove0.3510.0280.790
omnipath_cache_save0.7620.0201.904
omnipath_cache_search0.0000.0020.001
omnipath_cache_set_ext0.2260.0080.460
omnipath_cache_update_status0.2790.0160.599
omnipath_cache_wipe0.0000.0000.001
omnipath_get_config_path0.0000.0010.001
omnipath_load_config0.0010.0000.000
omnipath_log0.0000.0000.001
omnipath_logfile0.0020.0000.014
omnipath_msg0.0190.0000.030
omnipath_reset_config0.0010.0000.001
omnipath_save_config000
omnipath_set_cachedir0.0730.0010.074
omnipath_set_console_loglevel0.0010.0010.003
omnipath_set_logfile_loglevel0.0000.0020.003
omnipath_set_loglevel0.0010.0020.013
omnipath_show_db0.1480.0040.152
omnipath_unlock_cache_db0.0010.0000.001
only_from0.0000.0000.001
ontology_ensure_id0.0020.0000.017
ontology_ensure_name0.0020.0000.001
ontology_name_id0.0020.0000.002
pathwaycommons_download0.0020.0000.016
pivot_annotations17.466 1.33140.047
preppi_download0.0010.0000.001
preppi_filter0.0020.0000.018
print_bma_motif_es0.5840.0462.136
print_bma_motif_vs0.3370.0091.349
print_interactions10.297 0.65319.885
print_path_es0.7230.1222.732
print_path_vs2.5640.1405.963
pubmed_open 7.635 0.45210.225
query_info0.1930.0290.584
ramilowski_download0.0020.0000.001
regnetwork_directions0.0010.0000.001
regnetwork_download0.0010.0000.002
relations_list_to_table0.1610.0040.180
relations_table_to_graph000
relations_table_to_list0.1150.0030.120
remap_dorothea_download0.0010.0000.000
remap_filtered000
remap_tf_target_download000
resource_info0.2340.0680.967
resources_colname0.7940.1212.726
simplify_intercell_network0.0010.0000.002
swap_relations0.1410.0040.146
swissprots_only0.0670.0040.071
tfcensus_download0.4240.0160.582
translate_ids0.0010.0000.002
trembls_only0.0600.0000.059
trrust_download0.0000.0010.002
uniprot_full_id_mapping_table0.0000.0020.002
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.001
uniprot_id_type0.0080.0000.009
uniprot_idmapping_id_types0.3270.0041.322
unique_intercell_network0.0020.0000.002
unnest_evidences0.0000.0000.001
uploadlists_id_type0.0050.0040.008
vinayagam_download0.0010.0000.001
walk_ontology_tree0.0020.0000.002
with_extra_attrs7.0940.1579.420
with_references0.6580.0552.575
zenodo_download0.0010.0000.002