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This page was generated on 2023-05-10 10:04:36 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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CHECK results for OmnipathR on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1399/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.9.0  (landing page)
Denes Turei
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 May 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 7cebd4a
git_last_commit_date: 2023-04-25 15:13:16 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: OmnipathR
Version: 3.9.0
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_3.9.0.tar.gz
StartedAt: 2023-05-09 23:31:38 -0000 (Tue, 09 May 2023)
EndedAt: 2023-05-09 23:59:44 -0000 (Tue, 09 May 2023)
EllapsedTime: 1686.3 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_3.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.9.0’
* 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 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
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-09 23:31:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:31:53] [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
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-09 23:32:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:32:04] [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                49.461  0.047  51.403
curated_ligrec_stats                 43.272  1.593 180.300
filter_extra_attrs                   33.657  0.064  35.059
extra_attr_values                    22.195  0.215  24.385
extra_attrs_to_cols                  21.184  0.060  21.245
with_extra_attrs                     17.501  0.268  19.837
extra_attrs                          14.250  0.116  14.366
nichenet_gr_network_omnipath         13.966  0.205  16.236
has_extra_attrs                      13.793  0.272  14.066
pivot_annotations                    12.318  0.798  24.044
giant_component                      12.821  0.259  15.161
go_annot_download                    10.226  0.917  19.131
nichenet_signaling_network_omnipath  10.189  0.152  12.628
filter_by_resource                    8.257  0.124  14.273
find_all_paths                        7.847  0.000   7.847
filter_intercell                      7.168  0.293  12.812
curated_ligand_receptor_interactions  6.944  0.191  26.808
print_interactions                    6.734  0.307  16.488
pubmed_open                           6.456  0.461   8.919
get_signed_ptms                       6.611  0.180   8.091
collectri                             4.750  0.089   7.068
dorothea                              2.594  0.112   5.872
print_path_vs                         2.620  0.076   7.304
enzsub_graph                          2.566  0.036   5.818
database_summary                      1.992  0.604  12.604
import_all_interactions               2.258  0.165   6.841
import_transcriptional_interactions   2.176  0.084   5.546
import_kinaseextra_interactions       1.766  0.108   5.181
hpo_download                          1.648  0.111  10.483
annotated_network                     1.463  0.084   7.745
biomart_query                         1.361  0.060  16.364
import_mirnatarget_interactions       1.306  0.041   5.044
ensembl_id_mapping_table              1.006  0.048  22.865
* 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-devel_2023-03-12_r83975-bin/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
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Contains 16 files.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:54] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-08 21:56:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:56:56] [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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
[2023-05-09 23:45:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Contains 15 files.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-09 23:45:17] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 15.329   0.625  64.501

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.0260.0080.034
all_uniprots0.0140.0000.014
ancestors0.0070.0080.014
annotated_network1.4630.0847.745
annotation_categories49.461 0.04751.403
biomart_query 1.361 0.06016.364
bioplex10.0150.0000.014
bioplex20.0110.0040.014
bioplex30.0140.0000.014
bioplex_all0.0150.0000.014
bioplex_hct116_10.0150.0000.015
bma_motif_es0.6260.0322.845
bma_motif_vs0.3210.0041.641
collectri4.7500.0897.068
common_name0.0660.0040.070
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table0.0110.0040.015
curated_ligand_receptor_interactions 6.944 0.19126.808
curated_ligrec_stats 43.272 1.593180.300
database_summary 1.992 0.60412.604
descendants0.0140.0000.015
dorothea2.5940.1125.872
ensembl_dataset0.0140.0000.014
ensembl_id_mapping_table 1.006 0.04822.865
ensembl_id_type0.0060.0000.006
ensembl_name0.1200.0000.121
ensembl_organisms0.2590.0000.260
ensembl_organisms_raw0.2470.0000.248
ensembl_orthology0.0000.0000.001
enzsub_graph2.5660.0365.818
evex_download0.0130.0040.018
evidences000
extra_attr_values22.195 0.21524.385
extra_attrs14.250 0.11614.366
extra_attrs_to_cols21.184 0.06021.245
filter_by_resource 8.257 0.12414.273
filter_extra_attrs33.657 0.06435.059
filter_intercell 7.168 0.29312.812
filter_intercell_network0.0270.0000.026
find_all_paths7.8470.0007.847
get_annotation_resources0.1960.0001.582
get_complex_genes1.2580.0483.495
get_complex_resources0.2490.0321.687
get_db000
get_enzsub_resources0.1930.0121.555
get_interaction_resources0.1970.0081.455
get_intercell_categories0.4490.0201.222
get_intercell_generic_categories0.0680.0000.068
get_intercell_resources0.1990.0041.576
get_ontology_db0.0140.0000.014
get_resources0.2050.0001.510
get_signed_ptms6.6110.1808.091
giant_component12.821 0.25915.161
go_annot_download10.226 0.91719.131
go_annot_slim000
go_ontology_download0.0140.0000.014
guide2pharma_download0.0140.0000.013
harmonizome_download0.0140.0000.013
has_extra_attrs13.793 0.27214.066
homologene_download0.0410.0030.044
homologene_raw0.0240.0040.027
homologene_uniprot_orthology0.0140.0010.014
homology_translate000
hpo_download 1.648 0.11110.483
htridb_download0.0140.0000.014
import_all_interactions2.2580.1656.841
import_intercell_network0.0180.0040.022
import_kinaseextra_interactions1.7660.1085.181
import_ligrecextra_interactions0.9720.0243.920
import_lncrna_mrna_interactions0.7050.0882.825
import_mirnatarget_interactions1.3060.0415.044
import_omnipath_annotations0.7500.0162.850
import_omnipath_complexes0.8230.0403.850
import_omnipath_enzsub1.3670.0242.707
import_omnipath_interactions0.3990.0041.700
import_omnipath_intercell0.6270.0681.870
import_pathwayextra_interactions1.2820.0564.446
import_post_translational_interactions0.9560.0403.958
import_small_molecule_protein_interactions0.4860.0401.286
import_tf_mirna_interactions0.8780.0483.575
import_tf_target_interactions1.4700.0564.468
import_transcriptional_interactions2.1760.0845.546
inbiomap_download000
inbiomap_raw000
interaction_datasets0.4830.0391.462
interaction_graph0.4700.0081.793
interaction_types0.0200.0040.023
intercell_categories0.0420.0000.042
intercell_consensus_filter1.4910.0763.560
is_ontology_id000
is_swissprot0.0430.0000.043
is_trembl0.0410.0000.041
is_uniprot0.0120.0040.016
kegg_info0.0150.0000.015
kegg_open0.0140.0000.014
kegg_pathway_annotations000
kegg_pathway_download0.0140.0000.014
kegg_pathway_list0.0140.0000.014
kegg_pathways_download000
kegg_picture0.2160.0161.120
kegg_process0.0230.0040.028
latin_name0.0620.0120.074
load_db0.1410.0040.146
ncbi_taxid0.0680.0000.069
nichenet_build_model000
nichenet_expression_data0.0160.0000.016
nichenet_gr_network0.0410.0000.041
nichenet_gr_network_evex0.0140.0000.013
nichenet_gr_network_harmonizome0.0150.0000.014
nichenet_gr_network_htridb0.0140.0000.013
nichenet_gr_network_omnipath13.966 0.20516.236
nichenet_gr_network_pathwaycommons0.0150.0000.014
nichenet_gr_network_regnetwork0.0140.0000.014
nichenet_gr_network_remap0.0140.0000.014
nichenet_gr_network_trrust0.0140.0000.014
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0370.0040.041
nichenet_lr_network_guide2pharma0.0140.0000.014
nichenet_lr_network_omnipath0.0420.0000.043
nichenet_lr_network_ramilowski0.0140.0000.014
nichenet_main000
nichenet_networks0.0630.0040.067
nichenet_optimization000
nichenet_remove_orphan_ligands0.0370.0040.041
nichenet_results_dir000
nichenet_signaling_network0.0560.0120.068
nichenet_signaling_network_cpdb0.0100.0040.014
nichenet_signaling_network_evex0.0100.0040.015
nichenet_signaling_network_harmonizome0.0140.0000.015
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath10.189 0.15212.628
nichenet_signaling_network_pathwaycommons0.0140.0000.014
nichenet_signaling_network_vinayagam0.0130.0000.014
nichenet_test000
nichenet_workarounds000
obo_parser0.0960.0201.202
omnipath4.8360.0084.844
omnipath_cache_autoclean000
omnipath_cache_clean0.0160.0040.020
omnipath_cache_clean_db0.1000.0040.104
omnipath_cache_download_ready0.7050.0561.483
omnipath_cache_filter_versions0.1470.0080.163
omnipath_cache_get0.1080.0040.113
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.0790.0040.085
omnipath_cache_load0.8640.0364.449
omnipath_cache_move_in0.2090.0200.232
omnipath_cache_remove0.1300.0120.146
omnipath_cache_save0.3440.0200.376
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1000.0040.107
omnipath_cache_update_status0.1210.0200.141
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.000
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0000.0010.001
omnipath_msg0.0060.0020.007
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0680.0040.073
omnipath_set_console_loglevel0.0000.0010.001
omnipath_set_logfile_loglevel0.0000.0010.001
omnipath_set_loglevel0.0010.0000.000
omnipath_show_db0.0750.0040.079
omnipath_unlock_cache_db0.0000.0000.001
ontology_ensure_id0.0000.0000.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0000.0010.001
pathwaycommons_download0.0000.0010.000
pivot_annotations12.318 0.79824.044
preppi_download000
preppi_filter0.0010.0000.001
print_bma_motif_es0.4200.0682.645
print_bma_motif_vs0.2890.0081.711
print_interactions 6.734 0.30716.488
print_path_es0.7120.0573.614
print_path_vs2.6200.0767.304
pubmed_open6.4560.4618.919
query_info0.1910.0081.002
ramilowski_download0.0010.0000.001
regnetwork_directions0.0010.0000.001
regnetwork_download000
relations_list_to_table0.1040.0000.327
relations_table_to_graph000
relations_table_to_list0.0820.0000.255
remap_dorothea_download0.0010.0000.000
remap_filtered0.0010.0000.000
remap_tf_target_download0.0000.0000.001
resource_info0.2530.0201.600
resources_colname0.7240.0483.090
simplify_intercell_network0.0010.0000.001
swap_relations0.0890.0170.277
swissprots_only0.040.000.04
tfcensus_download0.2880.0160.383
translate_ids0.0010.0000.001
trembls_only0.0350.0040.039
trrust_download0.0010.0000.001
uniprot_full_id_mapping_table0.0010.0000.000
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.000
uniprot_id_type0.0050.0000.006
unique_intercell_network0.0010.0000.001
uploadlists_id_type0.0020.0040.005
vinayagam_download000
walk_ontology_tree0.0010.0000.001
with_extra_attrs17.501 0.26819.837
with_references0.6360.0293.537
zenodo_download0.0010.0000.001