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 11:37:19 -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 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: 3.8.2
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_3.8.2.tar.gz
StartedAt: 2023-10-16 04:48:11 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 05:15:38 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 1646.3 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_3.8.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.8.2’
* 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 startup messages can be suppressed ... NOTE
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 04:48:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:48:48] [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
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 04:49:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 04:49:13] [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                            224.589  3.008 296.566
dorothea                             122.260  1.060 174.247
annotation_categories                101.585  0.482 129.382
curated_ligrec_stats                  51.344  2.797 118.537
filter_extra_attrs                    46.865  0.227  58.975
extra_attr_values                     26.517  0.569  65.928
nichenet_gr_network_omnipath          24.735  0.686  33.098
extra_attrs_to_cols                   23.543  0.266  44.411
giant_component                       21.369  0.489  27.354
with_extra_attrs                      20.435  0.361  28.916
pivot_annotations                     17.120  1.478  25.369
nichenet_signaling_network_omnipath   17.914  0.537  23.880
extra_attrs                           15.182  0.142  42.426
has_extra_attrs                       15.198  0.102  19.779
go_annot_download                     13.863  1.056  22.820
filter_by_resource                    12.510  0.359  16.486
print_interactions                    12.257  0.435  17.517
find_all_paths                        12.123  0.190  15.007
get_signed_ptms                       11.251  0.072  14.722
pubmed_open                            9.798  0.340  13.112
filter_intercell                       8.866  0.900  12.078
curated_ligand_receptor_interactions   8.318  0.651  17.236
omnipath                               8.561  0.039  11.360
database_summary                       3.744  3.103   9.492
import_transcriptional_interactions    4.922  0.186   7.344
print_path_vs                          4.453  0.152   7.382
enzsub_graph                           3.758  0.159  19.548
hpo_download                           3.459  0.378   5.035
biomart_query                          2.232  0.233  31.213
ensembl_id_mapping_table               1.461  0.127  25.262
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-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/4.3-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
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:01] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-15 15:51:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:02] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-10-15 15:51:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:51:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:06] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-15 15:51:06] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:06] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-15 15:51:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-15 15:51:07] [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-apple-darwin20 (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)
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] Contains 16 files.
[2023-10-16 05:14:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-16 05:14:16] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 19.436   1.869  44.645

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0020.002
all_uniprot_acs0.0440.0050.074
all_uniprots0.0230.0030.034
ancestors0.0220.0030.030
annotated_network1.7010.2184.265
annotation_categories101.585 0.482129.382
biomart_query 2.232 0.23331.213
bioplex10.0230.0030.033
bioplex20.0230.0020.027
bioplex30.0220.0020.033
bioplex_all0.0230.0020.030
bioplex_hct116_10.0220.0030.029
bma_motif_es0.5870.0871.500
bma_motif_vs0.2520.0110.867
collectri224.589 3.008296.566
common_name0.0590.0010.086
consensuspathdb_download0.0010.0020.002
consensuspathdb_raw_table0.0210.0030.033
curated_ligand_receptor_interactions 8.318 0.65117.236
curated_ligrec_stats 51.344 2.797118.537
database_summary3.7443.1039.492
descendants0.0220.0020.030
dorothea122.260 1.060174.247
ensembl_dataset0.0200.0020.057
ensembl_id_mapping_table 1.461 0.12725.262
ensembl_id_type0.0090.0010.031
ensembl_name0.1170.0020.381
ensembl_organisms0.3920.0071.302
ensembl_organisms_raw0.3830.0081.283
ensembl_orthology0.0010.0010.001
enzsub_graph 3.758 0.15919.548
evex_download0.0220.0030.059
evidences0.0000.0010.017
extra_attr_values26.517 0.56965.928
extra_attrs15.182 0.14242.426
extra_attrs_to_cols23.543 0.26644.411
filter_by_resource12.510 0.35916.486
filter_extra_attrs46.865 0.22758.975
filter_intercell 8.866 0.90012.078
filter_intercell_network0.0460.0050.062
find_all_paths12.123 0.19015.007
from_evidences0.0000.0010.002
get_annotation_resources0.1530.0120.677
get_complex_genes1.9490.1503.219
get_complex_resources0.1240.0070.733
get_db0.0000.0010.001
get_enzsub_resources0.1190.0060.618
get_interaction_resources0.1240.0120.730
get_intercell_categories0.5930.1201.076
get_intercell_generic_categories0.0420.0040.058
get_intercell_resources0.1240.0070.740
get_ontology_db0.0240.0020.033
get_resources0.1250.0120.757
get_signed_ptms11.251 0.07214.722
giant_component21.369 0.48927.354
go_annot_download13.863 1.05622.820
go_annot_slim0.0010.0010.001
go_ontology_download0.0210.0020.028
guide2pharma_download0.0210.0030.028
harmonizome_download0.0210.0030.027
has_extra_attrs15.198 0.10219.779
homologene_download0.0220.0030.032
homologene_raw0.0400.0040.054
homologene_uniprot_orthology0.0210.0020.029
homology_translate0.0000.0000.001
hpo_download3.4590.3785.035
htridb_download0.0230.0030.033
import_all_interactions0.8350.0892.335
import_intercell_network0.0230.0030.032
import_kinaseextra_interactions2.5420.1454.520
import_ligrecextra_interactions1.1740.1072.959
import_lncrna_mrna_interactions0.7700.0882.052
import_mirnatarget_interactions1.8760.1243.659
import_omnipath_annotations0.7690.0811.842
import_omnipath_complexes0.9450.0962.464
import_omnipath_enzsub2.4160.0173.693
import_omnipath_interactions0.4370.0101.121
import_omnipath_intercell0.7870.0931.447
import_pathwayextra_interactions1.4080.1182.992
import_post_translational_interactions1.4070.1182.957
import_small_molecule_protein_interactions0.7750.0751.297
import_tf_mirna_interactions1.2990.1072.773
import_tf_target_interactions2.6050.1294.557
import_transcriptional_interactions4.9220.1867.344
inbiomap_download0.0000.0020.001
inbiomap_raw0.0010.0000.001
interaction_datasets0.6640.0421.307
interaction_graph0.6650.0141.435
interaction_types0.0780.0040.104
intercell_categories0.0700.0050.101
intercell_consensus_filter2.0460.2163.323
is_ontology_id0.0000.0010.001
is_swissprot0.0610.0050.080
is_trembl0.0620.0050.083
is_uniprot0.0230.0030.036
kegg_info0.0230.0030.031
kegg_open0.0220.0030.029
kegg_pathway_annotations0.0010.0000.003
kegg_pathway_download0.0230.0030.029
kegg_pathway_list0.0220.0030.032
kegg_pathways_download0.0000.0010.002
kegg_picture0.1930.0751.652
kegg_process0.0430.0050.047
latin_name0.1170.0030.159
load_db0.1680.0070.224
ncbi_taxid0.1120.0020.145
nichenet_build_model0.0000.0010.004
nichenet_expression_data0.0230.0030.035
nichenet_gr_network0.1080.0080.159
nichenet_gr_network_evex0.0210.0020.029
nichenet_gr_network_harmonizome0.0230.0030.036
nichenet_gr_network_htridb0.0210.0020.031
nichenet_gr_network_omnipath24.735 0.68633.098
nichenet_gr_network_pathwaycommons0.0210.0030.034
nichenet_gr_network_regnetwork0.0220.0020.029
nichenet_gr_network_remap0.0220.0020.033
nichenet_gr_network_trrust0.0220.0020.030
nichenet_ligand_activities0.0000.0020.002
nichenet_ligand_target_links0.0010.0020.003
nichenet_ligand_target_matrix0.0000.0010.001
nichenet_lr_network0.0630.0050.090
nichenet_lr_network_guide2pharma0.0210.0020.028
nichenet_lr_network_omnipath0.0640.0060.089
nichenet_lr_network_ramilowski0.0210.0030.031
nichenet_main0.0000.0010.001
nichenet_networks0.1060.0110.157
nichenet_optimization0.0010.0000.001
nichenet_remove_orphan_ligands0.0640.0050.091
nichenet_results_dir000
nichenet_signaling_network0.0680.0070.095
nichenet_signaling_network_cpdb0.0210.0030.033
nichenet_signaling_network_evex0.0220.0020.035
nichenet_signaling_network_harmonizome0.0220.0020.030
nichenet_signaling_network_inbiomap0.0010.0010.001
nichenet_signaling_network_omnipath17.914 0.53723.880
nichenet_signaling_network_pathwaycommons0.0230.0020.032
nichenet_signaling_network_vinayagam0.0220.0030.028
nichenet_test000
nichenet_workarounds0.0000.0010.001
obo_parser0.2170.0132.189
omnipath 8.561 0.03911.360
omnipath_cache_autoclean0.0000.0010.001
omnipath_cache_clean0.0140.0010.018
omnipath_cache_clean_db0.1850.0120.231
omnipath_cache_download_ready0.9250.0751.235
omnipath_cache_filter_versions0.2490.0260.345
omnipath_cache_get0.1820.0220.248
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1410.0170.218
omnipath_cache_load0.9770.0512.301
omnipath_cache_move_in0.3690.0440.525
omnipath_cache_remove0.2150.0280.308
omnipath_cache_save0.3560.0370.660
omnipath_cache_search0.0010.0010.005
omnipath_cache_set_ext0.1690.0230.246
omnipath_cache_update_status0.1970.0240.271
omnipath_cache_wipe0.0000.0010.001
omnipath_get_config_path0.0010.0010.005
omnipath_load_config0.0000.0010.000
omnipath_log0.0000.0010.001
omnipath_logfile0.0010.0000.002
omnipath_msg0.0110.0020.016
omnipath_reset_config0.0010.0000.001
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0550.0060.070
omnipath_set_console_loglevel0.0020.0010.003
omnipath_set_logfile_loglevel0.0020.0010.003
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.1250.0020.160
omnipath_unlock_cache_db0.0000.0010.001
only_from0.0000.0000.001
ontology_ensure_id0.0010.0010.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0010.002
pathwaycommons_download0.0010.0010.002
pivot_annotations17.120 1.47825.369
preppi_download0.0010.0010.005
preppi_filter0.0010.0000.002
print_bma_motif_es0.3480.0801.200
print_bma_motif_vs0.2020.0090.799
print_interactions12.257 0.43517.517
print_path_es0.8960.0922.151
print_path_vs4.4530.1527.382
pubmed_open 9.798 0.34013.112
query_info0.1170.0140.540
ramilowski_download0.0010.0020.002
regnetwork_directions0.0010.0010.002
regnetwork_download0.0010.0010.001
relations_list_to_table0.1700.0060.197
relations_table_to_graph0.0000.0000.001
relations_table_to_list0.1380.0070.184
remap_dorothea_download0.0000.0010.002
remap_filtered0.0010.0010.001
remap_tf_target_download0.0000.0010.003
resource_info0.2540.2011.079
resources_colname0.9050.1271.873
simplify_intercell_network0.0010.0010.002
swap_relations0.1560.0060.215
swissprots_only0.0620.0020.087
tfcensus_download0.3200.0233.554
translate_ids0.0020.0010.002
trembls_only0.0610.0010.066
trrust_download0.0010.0010.002
uniprot_full_id_mapping_table0.0010.0010.003
uniprot_genesymbol_cleanup0.0000.0010.001
uniprot_id_mapping_table0.0010.0010.002
uniprot_id_type0.0090.0000.014
uniprot_idmapping_id_types0.2880.0150.911
unique_intercell_network0.0010.0010.002
unnest_evidences0.0010.0010.001
uploadlists_id_type0.0090.0010.012
vinayagam_download0.0010.0000.002
walk_ontology_tree0.0010.0010.002
with_extra_attrs20.435 0.36128.916
with_references0.7470.0921.827
zenodo_download0.0020.0010.008