Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 1467/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.12.4  (landing page)
Denes Turei
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: edb3c69
git_last_commit_date: 2024-10-02 06:46:04 -0400 (Wed, 02 Oct 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

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: 3.12.4
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.4.tar.gz
StartedAt: 2024-10-17 03:14:25 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 03:45:23 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 1857.9 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.4’
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 03:14:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:44] [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
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:14:54] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_organisms: no visible binding for global variable ‘ncbi_tax_id’
Undefined global functions or variables:
  ncbi_tax_id
* 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                            143.273  2.016 151.583
annotation_categories                 85.846  0.070  89.068
dorothea                              71.172  1.217  79.011
curated_ligrec_stats                  45.217  3.260 146.122
static_table                          10.455 12.436 118.918
nichenet_gr_network_omnipath          19.049  0.286  22.591
filter_extra_attrs                    18.073  0.270  19.227
go_annot_download                     15.978  1.114  28.783
extra_attr_values                     16.084  0.736  21.734
pivot_annotations                     15.385  1.292  50.717
with_extra_attrs                      15.336  0.865  32.740
nichenet_signaling_network_omnipath   14.153  0.371  22.040
extra_attrs_to_cols                   14.167  0.175  14.342
giant_component                       13.133  0.231  21.543
pubmed_open                            9.190  0.520  17.297
has_extra_attrs                        9.538  0.129  10.098
print_interactions                     9.085  0.443  21.162
filter_intercell                       8.223  0.679  14.419
filter_by_resource                     7.801  0.455  11.641
curated_ligand_receptor_interactions   6.490  0.795  22.303
resources_in                           6.225  0.054  13.015
find_all_paths                         5.927  0.075   6.003
get_signed_ptms                        5.266  0.022   6.405
extra_attrs                            5.108  0.047   5.154
hpo_download                           3.741  0.383  29.891
import_transcriptional_interactions    3.555  0.317   8.288
print_path_vs                          3.559  0.083   7.815
import_all_interactions                3.342  0.177   9.724
import_tf_target_interactions          2.259  0.187   5.122
enzsub_graph                           2.257  0.072   5.187
intercell_consensus_filter             2.057  0.207   5.276
import_kinaseextra_interactions        1.659  0.286   7.155
ensembl_id_mapping_table               1.851  0.064  27.489
import_mirnatarget_interactions        1.801  0.085   5.251
annotated_network                      1.664  0.115   7.712
biomart_query                          1.059  0.068   9.032
kegg_picture                           0.246  0.016   5.046
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Contains 6 files.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:38] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-16 16:21:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-16 16:21:40] [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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:57] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Contains 17 files.
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 03:34:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 03:34:58] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 21.662   1.993  72.471

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0010.001
all_uniprot_acs0.0190.0000.019
all_uniprots0.010.000.01
ancestors0.0090.0000.009
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bioplex10.0050.0080.013
bioplex20.0080.0040.012
bioplex30.0070.0040.012
bioplex_all0.0120.0000.013
bioplex_hct116_10.0700.0000.071
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common_name0.0520.0000.051
consensuspathdb_download0.0000.0000.001
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descendants0.0130.0000.014
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ensembl_dataset0.0240.0000.024
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ensembl_id_type0.0050.0000.005
ensembl_name0.1640.0000.165
ensembl_organisms0.2930.0080.301
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enzsub_graph2.2570.0725.187
evex_download0.0140.0000.015
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extra_attrs5.1080.0475.154
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get_complex_genes1.2510.0923.865
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get_db0.0010.0000.000
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get_intercell_resources0.1510.0000.837
get_ontology_db0.0100.0040.014
get_resources0.1430.0010.829
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giant_component13.133 0.23121.543
go_annot_download15.978 1.11428.783
go_annot_slim000
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guide2pharma_download0.0170.0000.017
harmonizome_download0.0170.0000.017
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homologene_download0.0190.0040.023
homologene_raw0.0410.0030.044
homologene_uniprot_orthology0.0220.0000.022
hpo_download 3.741 0.38329.891
htridb_download0.0140.0090.023
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import_intercell_network0.0180.0080.025
import_kinaseextra_interactions1.6590.2867.155
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import_mirnatarget_interactions1.8010.0855.251
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import_omnipath_enzsub2.1770.0234.323
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import_pathwayextra_interactions1.4800.0914.298
import_post_translational_interactions1.8700.1304.758
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import_tf_target_interactions2.2590.1875.122
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kegg_pathway_list0.0340.0000.034
kegg_pathways_download0.0000.0010.001
kegg_picture0.2460.0165.046
kegg_process0.0460.0080.142
latin_name0.1190.0040.124
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nichenet_main0.0010.0000.001
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nichenet_signaling_network_vinayagam0.0130.0000.013
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nichenet_workarounds000
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oma_pairwise0.0210.0000.021
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omnipath_cache_get0.1150.0040.122
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omnipath_cache_save0.3330.0080.622
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omnipath_msg0.0110.0020.013
omnipath_reset_config0.0000.0000.001
omnipath_save_config000
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omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.1020.0000.118
omnipath_unlock_cache_db0.0010.0000.001
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ontology_ensure_id0.0000.0020.018
ontology_ensure_name0.0000.0010.001
ontology_name_id0.0010.0000.001
organism_for0.0940.0000.142
pathwaycommons_download0.0020.0000.002
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preppi_download0.0010.0000.003
preppi_filter0.0020.0000.001
print_bma_motif_es0.3950.0441.822
print_bma_motif_vs0.2460.0120.942
print_interactions 9.085 0.44321.162
print_path_es0.9340.0263.310
print_path_vs3.5590.0837.815
pubmed_open 9.190 0.52017.297
query_info0.2280.0120.652
ramilowski_download0.0010.0000.001
regnetwork_directions0.0020.0000.014
regnetwork_download0.0010.0000.002
relations_list_to_table0.1720.0000.550
relations_table_to_graph000
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remap_dorothea_download0.0000.0020.002
remap_filtered0.0000.0000.001
remap_tf_target_download0.0000.0000.001
resource_info0.3090.0811.300
resources_colname0.9910.0263.355
resources_in 6.225 0.05413.015
show_network000
simplify_intercell_network0.0000.0030.018
static_table 10.455 12.436118.918
static_tables0.1300.0130.416
swap_relations0.1740.0320.546
swissprots_only0.0790.0010.121
tfcensus_download0.3790.1051.023
translate_ids0.0050.0000.018
trembls_only0.0700.0340.137
trrust_download0.0020.0000.002
uniprot_full_id_mapping_table0.0020.0000.004
uniprot_genesymbol_cleanup0.0000.0010.001
uniprot_id_mapping_table0.0000.0020.005
uniprot_id_type0.0030.0040.014
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unique_intercell_network0.0020.0000.002
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vinayagam_download0.0010.0000.002
walk_ontology_tree0.0020.0000.002
with_extra_attrs15.336 0.86532.740
with_references1.0810.0573.921
zenodo_download0.0030.0000.007