Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2024-03-06 11:33:17 -0500 (Wed, 06 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
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 1452/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.10.1  (landing page)
Denes Turei
Snapshot Date: 2024-03-05 14:05:04 -0500 (Tue, 05 Mar 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_18
git_last_commit: b1b2bab
git_last_commit_date: 2023-10-25 11:47:10 -0500 (Wed, 25 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for OmnipathR on nebbiolo2


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: 3.10.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings OmnipathR_3.10.1.tar.gz
StartedAt: 2024-03-06 00:43:55 -0500 (Wed, 06 Mar 2024)
EndedAt: 2024-03-06 01:13:32 -0500 (Wed, 06 Mar 2024)
EllapsedTime: 1776.4 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings OmnipathR_3.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.10.1’
* 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
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-06 00:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:15] [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
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-06 00:44:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 00:44:25] [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
collectri                              113.298  1.656 119.103
dorothea                                68.430  1.356  75.753
annotation_categories                   64.911  0.076  66.580
curated_ligrec_stats                    43.734  3.923 135.598
filter_extra_attrs                      28.527  0.884  33.598
nichenet_signaling_network_omnipath     27.109  0.425  47.532
nichenet_gr_network_omnipath            19.825  0.423  25.728
go_annot_download                       17.982  0.821  33.470
pivot_annotations                       16.718  0.584  41.189
with_extra_attrs                        15.756  0.472  33.352
extra_attrs_to_cols                     16.057  0.170  16.619
giant_component                         11.825  0.336  18.606
extra_attr_values                       11.026  0.085  15.035
static_table                             9.440  0.795  78.362
pubmed_open                              8.963  0.727  12.377
curated_ligand_receptor_interactions     8.319  0.829  25.386
filter_intercell                         8.799  0.335  14.393
print_interactions                       8.393  0.354  24.654
has_extra_attrs                          7.853  0.199   8.058
get_signed_ptms                          7.639  0.248   9.613
filter_by_resource                       5.752  0.162   7.840
extra_attrs                              5.409  0.038   5.446
import_transcriptional_interactions      4.885  0.376   9.593
print_path_vs                            4.118  0.132  12.783
hpo_download                             3.108  0.349   6.617
enzsub_graph                             3.264  0.050   6.901
import_all_interactions                  2.892  0.211   8.945
import_tf_target_interactions            2.794  0.214   6.591
database_summary                         2.295  0.132   5.076
import_kinaseextra_interactions          2.282  0.113   7.196
annotated_network                        1.808  0.261   8.047
import_post_translational_interactions   1.484  0.116   6.176
import_pathwayextra_interactions         1.428  0.148   6.644
ensembl_id_mapping_table                 1.230  0.045  34.431
kegg_picture                             0.237  0.015   5.003
* 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-3.18-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Contains 6 files.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-05 15:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-05 15:33:07] [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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
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)
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Contains 17 files.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 01:02:48] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 19.353   1.517  57.443

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.020.000.02
all_uniprots0.0110.0000.010
ancestors0.0100.0000.009
annotated_network1.8080.2618.047
annotation_categories64.911 0.07666.580
biomart_query0.6190.0413.921
bioplex10.0110.0000.011
bioplex20.010.000.01
bioplex30.010.000.01
bioplex_all0.0370.0000.037
bioplex_hct116_10.0110.0000.012
bma_motif_es0.4010.0231.469
bma_motif_vs0.1870.0040.950
collectri113.298 1.656119.103
common_name0.0180.0000.019
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.010.000.01
curated_ligand_receptor_interactions 8.319 0.82925.386
curated_ligrec_stats 43.734 3.923135.598
database_summary2.2950.1325.076
descendants0.0270.0000.027
dorothea68.430 1.35675.753
ensembl_dataset0.0150.0000.014
ensembl_id_mapping_table 1.230 0.04534.431
ensembl_id_type0.0050.0000.004
ensembl_name0.0950.0000.095
ensembl_organisms0.2630.0000.342
ensembl_organisms_raw0.2560.0000.275
ensembl_orthology000
enzsub_graph3.2640.0506.901
evex_download0.0260.0040.030
evidences0.0010.0000.000
extra_attr_values11.026 0.08515.035
extra_attrs5.4090.0385.446
extra_attrs_to_cols16.057 0.17016.619
filter_by_resource5.7520.1627.840
filter_extra_attrs28.527 0.88433.598
filter_intercell 8.799 0.33514.393
filter_intercell_network0.0320.0000.032
find_all_paths4.4200.0064.548
from_evidences000
get_annotation_resources0.1380.0000.819
get_complex_genes2.3110.2104.379
get_complex_resources0.1900.0120.957
get_db0.0000.0000.001
get_enzsub_resources0.2170.0040.978
get_interaction_resources0.2200.0081.223
get_intercell_categories0.6410.0451.191
get_intercell_generic_categories0.0940.0160.173
get_intercell_resources0.1930.0040.992
get_ontology_db0.0260.0000.057
get_resources0.1990.0161.024
get_signed_ptms7.6390.2489.613
giant_component11.825 0.33618.606
go_annot_download17.982 0.82133.470
go_annot_slim0.0000.0000.001
go_ontology_download0.0230.0000.024
guide2pharma_download0.0210.0000.021
harmonizome_download0.0210.0000.020
has_extra_attrs7.8530.1998.058
homologene_download0.010.000.01
homologene_raw0.0140.0040.018
homologene_uniprot_orthology0.0070.0040.011
hpo_download3.1080.3496.617
htridb_download0.0290.0000.062
import_all_interactions2.8920.2118.945
import_intercell_network0.0190.0040.039
import_kinaseextra_interactions2.2820.1137.196
import_ligrecextra_interactions1.3740.0993.737
import_lncrna_mrna_interactions1.0700.0633.147
import_mirnatarget_interactions1.8970.1044.896
import_omnipath_annotations0.9400.0932.563
import_omnipath_complexes1.0610.1513.374
import_omnipath_enzsub1.6090.1292.500
import_omnipath_interactions0.4990.0241.499
import_omnipath_intercell0.9350.1273.365
import_pathwayextra_interactions1.4280.1486.644
import_post_translational_interactions1.4840.1166.176
import_small_molecule_protein_interactions0.8280.0482.777
import_tf_mirna_interactions1.2710.1084.683
import_tf_target_interactions2.7940.2146.591
import_transcriptional_interactions4.8850.3769.593
inbiomap_download000
inbiomap_raw000
interaction_datasets1.0460.0541.459
interaction_graph0.7700.0401.494
interaction_types0.1190.0000.119
intercell_categories0.1410.0040.145
intercell_consensus_filter1.5830.1493.589
is_ontology_id0.0010.0000.000
is_swissprot0.0860.0000.086
is_trembl0.0770.0000.077
is_uniprot0.0350.0000.035
kegg_info0.0310.0000.031
kegg_open0.0220.0080.030
kegg_pathway_annotations000
kegg_pathway_download0.0240.0080.032
kegg_pathway_list0.0290.0000.029
kegg_pathways_download0.0010.0000.001
kegg_picture0.2370.0155.003
kegg_process0.0490.0040.101
latin_name0.0980.0000.147
load_db0.1450.0080.153
ncbi_taxid0.0820.0000.083
nichenet_build_model000
nichenet_expression_data0.0240.0000.024
nichenet_gr_network0.0610.0000.060
nichenet_gr_network_evex0.0220.0000.022
nichenet_gr_network_harmonizome0.0240.0000.025
nichenet_gr_network_htridb0.0190.0040.022
nichenet_gr_network_omnipath19.825 0.42325.728
nichenet_gr_network_pathwaycommons0.0270.0000.043
nichenet_gr_network_regnetwork0.0260.0000.058
nichenet_gr_network_remap0.0300.0000.062
nichenet_gr_network_trrust0.0170.0040.021
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0650.0040.084
nichenet_lr_network_guide2pharma0.0230.0050.099
nichenet_lr_network_omnipath0.0810.0000.217
nichenet_lr_network_ramilowski0.1490.0000.413
nichenet_main0.0000.0000.029
nichenet_networks0.1180.0070.431
nichenet_optimization000
nichenet_remove_orphan_ligands0.0790.0000.271
nichenet_results_dir000
nichenet_signaling_network0.0710.0080.283
nichenet_signaling_network_cpdb0.0280.0000.121
nichenet_signaling_network_evex0.0260.0000.071
nichenet_signaling_network_harmonizome0.0260.0040.107
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath27.109 0.42547.532
nichenet_signaling_network_pathwaycommons0.0130.0080.021
nichenet_signaling_network_vinayagam0.0230.0000.023
nichenet_test0.0010.0000.000
nichenet_workarounds000
obo_parser0.1980.0000.494
oma_code0.030.000.03
oma_organisms0.0630.0000.063
oma_pairwise0.0140.0000.014
omnipath4.2370.0574.684
omnipath_cache_autoclean000
omnipath_cache_clean0.0110.0000.024
omnipath_cache_clean_db0.1490.0040.217
omnipath_cache_download_ready0.8290.0651.137
omnipath_cache_filter_versions0.1770.0160.196
omnipath_cache_get0.1530.0170.170
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1220.0040.126
omnipath_cache_load1.1460.0323.740
omnipath_cache_move_in0.3470.0480.534
omnipath_cache_remove0.2300.0040.318
omnipath_cache_save0.4170.0450.712
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1670.0200.338
omnipath_cache_update_status0.1870.0200.239
omnipath_cache_wipe0.0010.0000.000
omnipath_get_config_path0.0000.0010.001
omnipath_load_config000
omnipath_log0.0000.0010.000
omnipath_logfile0.0010.0010.001
omnipath_msg0.0130.0000.029
omnipath_reset_config000
omnipath_save_config0.0010.0000.001
omnipath_set_cachedir0.0560.0040.124
omnipath_set_console_loglevel0.0020.0000.002
omnipath_set_logfile_loglevel0.0020.0000.002
omnipath_set_loglevel0.0010.0000.001
omnipath_show_db0.1110.0000.159
omnipath_unlock_cache_db0.0000.0000.016
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0010.0000.001
pathwaycommons_download000
pivot_annotations16.718 0.58441.189
preppi_download0.0010.0000.002
preppi_filter0.0010.0000.002
print_bma_motif_es0.3080.0241.340
print_bma_motif_vs0.2160.0000.975
print_interactions 8.393 0.35424.654
print_path_es1.1820.0874.903
print_path_vs 4.118 0.13212.783
pubmed_open 8.963 0.72712.377
query_info0.1940.0040.578
ramilowski_download0.0010.0000.001
regnetwork_directions0.0010.0000.001
regnetwork_download0.0010.0000.001
relations_list_to_table0.1310.0000.169
relations_table_to_graph0.0010.0000.000
relations_table_to_list0.0720.0200.095
remap_dorothea_download0.0010.0000.001
remap_filtered000
remap_tf_target_download000
resource_info0.2490.0371.013
resources_colname0.8630.1353.242
show_network000
simplify_intercell_network0.0030.0000.003
static_table 9.440 0.79578.362
static_tables0.1030.0080.119
swap_relations0.1220.0080.133
swissprots_only0.0440.0000.045
tfcensus_download0.2510.0080.415
translate_ids0.0010.0000.001
trembls_only0.0320.0000.032
trrust_download0.0010.0000.001
uniprot_full_id_mapping_table0.0000.0000.001
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.001
uniprot_id_type0.0030.0000.002
uniprot_idmapping_id_types0.3870.0323.503
unique_intercell_network0.0000.0020.002
unnest_evidences000
uploadlists_id_type0.0020.0030.005
vinayagam_download0.0000.0010.002
walk_ontology_tree0.0000.0020.002
with_extra_attrs15.756 0.47233.352
with_references0.8300.0963.228
zenodo_download0.0010.0000.001