Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1456/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.14.0  (landing page)
Denes Turei
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_20
git_last_commit: 3c7d7f1
git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for OmnipathR on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: OmnipathR
Version: 3.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
StartedAt: 2024-11-20 10:39:59 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:58:26 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 1107.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 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
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [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
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [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                103.965  0.052 105.571
curated_ligrec_stats                  33.238  0.761 129.534
omnipath-interactions                 29.387  1.069  74.238
filter_extra_attrs                    25.706  0.176  27.998
nichenet_gr_network_omnipath          15.630  0.344  26.874
extra_attr_values                     14.657  0.419  17.580
go_annot_download                     13.863  0.511  27.881
extra_attrs_to_cols                   12.950  0.108  13.092
giant_component                       12.112  0.484  14.230
pivot_annotations                     11.173  0.313  22.058
with_extra_attrs                      10.994  0.127  12.633
nichenet_signaling_network_omnipath   10.493  0.071  14.170
omnipath_for_cosmos                   10.246  0.191  63.700
extra_attrs                            8.260  0.119   8.401
translate_ids_multi                    8.236  0.028  17.533
has_extra_attrs                        7.883  0.087   8.375
filter_by_resource                     7.221  0.136   8.708
filter_intercell                       6.877  0.202  10.634
static_table                           6.677  0.147  11.387
find_all_paths                         6.429  0.032   6.472
print_interactions                     6.349  0.092  10.288
signed_ptms                            5.569  0.004   6.620
curated_ligand_receptor_interactions   5.354  0.176  17.879
hpo_download                           2.437  0.226  25.027
enzsub_graph                           2.406  0.096   5.060
print_path_vs                          2.295  0.024   5.623
translate_ids                          1.347  0.004  20.189
ensembl_id_mapping_table               1.284  0.048  10.621
biomart_query                          0.969  0.020   5.515
all_uniprots                           0.878  0.055  26.050
uniprot_full_id_mapping_table          0.911  0.016  96.042
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package textcomp Error: Symbol \textrightarrow not provided by
(textcomp)                font family ptm in TS1 encoding.
(textcomp)                Default family used instead.

See the textcomp package documentation for explanation.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Contains 6 files.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:54] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:04:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:04:57] [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: aarch64-unknown-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)
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Contains 21 files.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:57:19] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 13.074   1.090  52.312

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0220.0000.022
all_uniprots 0.878 0.05526.050
ancestors0.0110.0000.011
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bioplex30.0570.0000.057
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descendants0.0130.0000.013
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evex_download0.0110.0000.011
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giant_component12.112 0.48414.230
go_annot_download13.863 0.51127.881
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harmonizome_download0.0120.0000.012
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hmdb_metabolite_fields0.0010.0000.001
hmdb_protein_fields0.0000.0000.001
hmdb_table0.0490.0000.049
homologene_download0.0110.0000.011
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htridb_download0.0120.0000.013
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kegg_pathways_download000
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kegg_process0.0200.0080.056
latin_name0.0820.0080.152
load_db0.1170.0000.124
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nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
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nichenet_optimization000
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nichenet_signaling_network_inbiomap000
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nichenet_signaling_network_vinayagam0.0110.0000.011
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omnipath_cache_wipe000
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omnipath_set_loglevel0.0030.0000.002
omnipath_show_db0.0710.0000.071
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ontology_ensure_name0.0010.0000.000
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organism_for0.0530.0000.053
pathwaycommons_download000
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preppi_download0.0010.0000.001
preppi_filter0.0010.0000.001
print_bma_motif_es0.4650.0441.928
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print_interactions 6.349 0.09210.288
print_path_es0.5070.0202.612
print_path_vs2.2950.0245.623
pubmed_open4.6750.0084.689
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ramilowski_download0.0010.0000.001
ramp_id_mapping_table0.0010.0000.001
ramp_id_type0.0030.0000.003
ramp_sqlite0.0010.0000.000
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regnetwork_download0.0010.0000.001
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relations_table_to_graph000
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remap_dorothea_download000
remap_filtered000
remap_tf_target_download0.0000.0000.001
resource_info0.1540.0131.148
resources0.0660.0001.003
resources_colname0.6020.0232.257
resources_in4.3110.0044.327
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simplify_intercell_network0.0010.0000.001
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static_tables0.0570.0000.260
stitch_actions0.0010.0000.001
stitch_links0.0010.0000.001
stitch_network0.0010.0000.001
stitch_remove_prefixes0.0080.0000.008
swap_relations0.0930.0000.342
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tfcensus_download0.2550.0000.285
translate_ids 1.347 0.00420.189
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trembls_only0.0390.0000.040
trrust_download0.0000.0000.001
uniprot_full_id_mapping_table 0.911 0.01696.042
uniprot_genesymbol_cleanup000
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uniprot_id_type0.0030.0000.003
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unique_intercell_network0.0010.0000.001
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vinayagam_download000
walk_ontology_tree0.0010.0000.001
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with_references0.4410.0242.166
zenodo_download0.0020.0000.001