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) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (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 1467/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.12.4 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: OmnipathR |
| Version: 3.12.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.4.tar.gz |
| StartedAt: 2024-10-17 10:17:17 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 10:45:50 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 1713.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.4’
* 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 whether startup messages can be suppressed ... NOTE
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:17:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 10:17:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:17:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:18:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:00] [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 10:18:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:18:27] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 10:18:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:18:27] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-17 10:18:27] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 10:18:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:18:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:18:28] [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 299.545 2.708 342.552
dorothea 160.893 1.748 209.019
annotation_categories 100.634 0.631 116.365
curated_ligrec_stats 55.831 2.207 122.655
filter_extra_attrs 52.115 0.308 62.238
extra_attr_values 29.808 0.540 59.486
nichenet_gr_network_omnipath 25.826 0.754 30.076
extra_attrs_to_cols 25.173 0.267 29.032
giant_component 21.428 0.604 42.179
with_extra_attrs 21.450 0.367 25.673
nichenet_signaling_network_omnipath 19.905 0.500 22.729
go_annot_download 16.806 1.403 25.119
pivot_annotations 16.121 1.447 22.039
extra_attrs 16.828 0.320 36.298
has_extra_attrs 16.026 0.195 18.667
filter_by_resource 13.542 0.305 16.008
print_interactions 12.791 0.399 16.702
find_all_paths 12.533 0.188 17.988
get_signed_ptms 12.315 0.155 22.636
pubmed_open 10.188 0.307 12.630
filter_intercell 9.523 0.889 20.234
omnipath 10.120 0.126 11.550
static_table 9.486 0.746 11.942
curated_ligand_receptor_interactions 9.540 0.453 18.401
resources_in 8.993 0.058 10.674
import_transcriptional_interactions 5.281 0.158 7.275
import_all_interactions 4.479 0.229 7.123
print_path_vs 4.405 0.109 7.136
enzsub_graph 4.109 0.142 10.530
annotated_network 2.890 0.254 6.904
get_complex_genes 2.198 0.128 5.661
ensembl_id_mapping_table 1.774 0.147 17.680
biomart_query 1.510 0.155 9.938
* 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 ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-10-16 16:05:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:08] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-16 16:05:08] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:08] [TRACE] [OmnipathR] Contains 1 files. [2024-10-16 16:05:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-16 16:05:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-16 16:05:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-16 16:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-16 16:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-16 16:05:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-16 16:05:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:11] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Contains 1 files. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-16 16:05:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-16 16:05:15] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
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-apple-darwin20
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 10:44:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:44:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:44:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 10:44:24] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:44:24] [TRACE] [OmnipathR] Contains 17 files.
[2024-10-17 10:44:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-17 10:44:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 10:44:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 10:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 10:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 10:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 10:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-17 10:44:25] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
21.379 1.588 49.089
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.002 | 0.003 | |
| all_uniprot_acs | 0.049 | 0.004 | 0.059 | |
| all_uniprots | 0.024 | 0.003 | 0.031 | |
| ancestors | 0.026 | 0.002 | 0.034 | |
| annotated_network | 2.890 | 0.254 | 6.904 | |
| annotation_categories | 100.634 | 0.631 | 116.365 | |
| biomart_query | 1.510 | 0.155 | 9.938 | |
| bioplex1 | 0.024 | 0.002 | 0.031 | |
| bioplex2 | 0.027 | 0.002 | 0.034 | |
| bioplex3 | 0.080 | 0.003 | 0.096 | |
| bioplex_all | 0.024 | 0.002 | 0.030 | |
| bioplex_hct116_1 | 0.025 | 0.002 | 0.032 | |
| bma_motif_es | 0.607 | 0.048 | 1.415 | |
| bma_motif_vs | 0.322 | 0.010 | 0.990 | |
| collectri | 299.545 | 2.708 | 342.552 | |
| common_name | 0.050 | 0.000 | 0.057 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.003 | |
| consensuspathdb_raw_table | 0.024 | 0.002 | 0.029 | |
| curated_ligand_receptor_interactions | 9.540 | 0.453 | 18.401 | |
| curated_ligrec_stats | 55.831 | 2.207 | 122.655 | |
| database_summary | 2.733 | 0.072 | 4.009 | |
| descendants | 0.025 | 0.002 | 0.031 | |
| dorothea | 160.893 | 1.748 | 209.019 | |
| ensembl_dataset | 0.017 | 0.001 | 0.021 | |
| ensembl_id_mapping_table | 1.774 | 0.147 | 17.680 | |
| ensembl_id_type | 0.004 | 0.001 | 0.017 | |
| ensembl_name | 0.100 | 0.002 | 0.222 | |
| ensembl_organisms | 0.292 | 0.007 | 0.716 | |
| ensembl_organisms_raw | 0.274 | 0.007 | 0.647 | |
| ensembl_orthology | 0.001 | 0.002 | 0.001 | |
| enzsub_graph | 4.109 | 0.142 | 10.530 | |
| evex_download | 0.026 | 0.003 | 0.067 | |
| evidences | 0.001 | 0.001 | 0.001 | |
| extra_attr_values | 29.808 | 0.540 | 59.486 | |
| extra_attrs | 16.828 | 0.320 | 36.298 | |
| extra_attrs_to_cols | 25.173 | 0.267 | 29.032 | |
| filter_by_resource | 13.542 | 0.305 | 16.008 | |
| filter_extra_attrs | 52.115 | 0.308 | 62.238 | |
| filter_intercell | 9.523 | 0.889 | 20.234 | |
| filter_intercell_network | 0.050 | 0.005 | 0.065 | |
| find_all_paths | 12.533 | 0.188 | 17.988 | |
| from_evidences | 0.000 | 0.001 | 0.001 | |
| get_annotation_resources | 0.133 | 0.008 | 0.649 | |
| get_complex_genes | 2.198 | 0.128 | 5.661 | |
| get_complex_resources | 0.193 | 0.007 | 0.910 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_enzsub_resources | 0.133 | 0.007 | 0.619 | |
| get_interaction_resources | 0.139 | 0.011 | 0.700 | |
| get_intercell_categories | 0.659 | 0.084 | 1.831 | |
| get_intercell_generic_categories | 0.077 | 0.005 | 0.171 | |
| get_intercell_resources | 0.200 | 0.005 | 0.803 | |
| get_ontology_db | 0.024 | 0.003 | 0.102 | |
| get_resources | 0.136 | 0.009 | 0.650 | |
| get_signed_ptms | 12.315 | 0.155 | 22.636 | |
| giant_component | 21.428 | 0.604 | 42.179 | |
| go_annot_download | 16.806 | 1.403 | 25.119 | |
| go_annot_slim | 0.000 | 0.002 | 0.002 | |
| go_ontology_download | 0.026 | 0.003 | 0.031 | |
| guide2pharma_download | 0.026 | 0.002 | 0.036 | |
| harmonizome_download | 0.024 | 0.002 | 0.028 | |
| has_extra_attrs | 16.026 | 0.195 | 18.667 | |
| homologene_download | 0.076 | 0.005 | 0.123 | |
| homologene_raw | 0.044 | 0.005 | 0.100 | |
| homologene_uniprot_orthology | 0.026 | 0.003 | 0.032 | |
| hpo_download | 3.537 | 0.400 | 4.661 | |
| htridb_download | 0.026 | 0.003 | 0.031 | |
| import_all_interactions | 4.479 | 0.229 | 7.123 | |
| import_intercell_network | 0.028 | 0.003 | 0.102 | |
| import_kinaseextra_interactions | 2.732 | 0.122 | 4.493 | |
| import_ligrecextra_interactions | 1.260 | 0.077 | 2.782 | |
| import_lncrna_mrna_interactions | 0.893 | 0.058 | 1.791 | |
| import_mirnatarget_interactions | 1.911 | 0.090 | 3.285 | |
| import_omnipath_annotations | 0.911 | 0.048 | 1.900 | |
| import_omnipath_complexes | 1.051 | 0.061 | 2.333 | |
| import_omnipath_enzsub | 2.496 | 0.021 | 3.428 | |
| import_omnipath_interactions | 0.505 | 0.012 | 1.239 | |
| import_omnipath_intercell | 0.887 | 0.063 | 1.503 | |
| import_pathwayextra_interactions | 1.460 | 0.088 | 2.799 | |
| import_post_translational_interactions | 1.520 | 0.087 | 2.866 | |
| import_small_molecule_protein_interactions | 0.816 | 0.044 | 1.245 | |
| import_tf_mirna_interactions | 1.349 | 0.072 | 2.541 | |
| import_tf_target_interactions | 2.711 | 0.099 | 4.173 | |
| import_transcriptional_interactions | 5.281 | 0.158 | 7.275 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0.000 | 0.001 | 0.000 | |
| interaction_datasets | 0.071 | 0.005 | 0.081 | |
| interaction_graph | 0.714 | 0.011 | 1.457 | |
| interaction_types | 0.073 | 0.004 | 0.084 | |
| intercell_categories | 0.110 | 0.005 | 0.132 | |
| intercell_consensus_filter | 2.112 | 0.173 | 3.129 | |
| is_ontology_id | 0.001 | 0.001 | 0.001 | |
| is_swissprot | 0.063 | 0.005 | 0.076 | |
| is_trembl | 0.067 | 0.005 | 0.079 | |
| is_uniprot | 0.028 | 0.002 | 0.035 | |
| kegg_info | 0.025 | 0.002 | 0.030 | |
| kegg_open | 0.024 | 0.002 | 0.029 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.025 | 0.003 | 0.032 | |
| kegg_pathway_list | 0.024 | 0.003 | 0.032 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
| kegg_picture | 0.139 | 0.013 | 1.515 | |
| kegg_process | 0.046 | 0.004 | 0.050 | |
| latin_name | 0.142 | 0.008 | 0.155 | |
| load_db | 0.163 | 0.005 | 0.179 | |
| ncbi_taxid | 0.099 | 0.001 | 0.111 | |
| nichenet_build_model | 0.001 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.024 | 0.002 | 0.030 | |
| nichenet_gr_network | 0.072 | 0.006 | 0.089 | |
| nichenet_gr_network_evex | 0.024 | 0.002 | 0.029 | |
| nichenet_gr_network_harmonizome | 0.025 | 0.003 | 0.039 | |
| nichenet_gr_network_htridb | 0.025 | 0.002 | 0.044 | |
| nichenet_gr_network_omnipath | 25.826 | 0.754 | 30.076 | |
| nichenet_gr_network_pathwaycommons | 0.093 | 0.005 | 0.106 | |
| nichenet_gr_network_regnetwork | 0.027 | 0.002 | 0.033 | |
| nichenet_gr_network_remap | 0.025 | 0.003 | 0.029 | |
| nichenet_gr_network_trrust | 0.026 | 0.003 | 0.034 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_links | 0.001 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0.000 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.076 | 0.006 | 0.090 | |
| nichenet_lr_network_guide2pharma | 0.026 | 0.003 | 0.034 | |
| nichenet_lr_network_omnipath | 0.072 | 0.006 | 0.088 | |
| nichenet_lr_network_ramilowski | 0.025 | 0.002 | 0.033 | |
| nichenet_main | 0.001 | 0.000 | 0.001 | |
| nichenet_networks | 0.114 | 0.011 | 0.142 | |
| nichenet_optimization | 0.001 | 0.000 | 0.000 | |
| nichenet_remove_orphan_ligands | 0.072 | 0.005 | 0.090 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.076 | 0.006 | 0.115 | |
| nichenet_signaling_network_cpdb | 0.025 | 0.002 | 0.030 | |
| nichenet_signaling_network_evex | 0.025 | 0.002 | 0.029 | |
| nichenet_signaling_network_harmonizome | 0.024 | 0.002 | 0.030 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 19.905 | 0.500 | 22.729 | |
| nichenet_signaling_network_pathwaycommons | 0.027 | 0.002 | 0.032 | |
| nichenet_signaling_network_vinayagam | 0.025 | 0.002 | 0.032 | |
| nichenet_test | 0.000 | 0.000 | 0.001 | |
| nichenet_workarounds | 0.001 | 0.001 | 0.001 | |
| obo_parser | 0.183 | 0.012 | 0.325 | |
| oma_code | 0.052 | 0.000 | 0.057 | |
| oma_organisms | 0.110 | 0.004 | 0.125 | |
| oma_pairwise | 0.024 | 0.003 | 0.181 | |
| oma_pairwise_genesymbols | 0.025 | 0.002 | 0.028 | |
| oma_pairwise_translated | 0.024 | 0.002 | 0.028 | |
| omnipath | 10.120 | 0.126 | 11.550 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.015 | 0.001 | 0.017 | |
| omnipath_cache_clean_db | 0.204 | 0.015 | 0.249 | |
| omnipath_cache_download_ready | 1.010 | 0.088 | 1.255 | |
| omnipath_cache_filter_versions | 0.239 | 0.026 | 0.327 | |
| omnipath_cache_get | 0.196 | 0.022 | 0.243 | |
| omnipath_cache_key | 0.002 | 0.001 | 0.002 | |
| omnipath_cache_latest_or_new | 0.146 | 0.016 | 0.184 | |
| omnipath_cache_load | 1.013 | 0.048 | 2.142 | |
| omnipath_cache_move_in | 0.388 | 0.048 | 0.485 | |
| omnipath_cache_remove | 0.234 | 0.025 | 0.295 | |
| omnipath_cache_save | 0.345 | 0.035 | 0.459 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.002 | |
| omnipath_cache_set_ext | 0.184 | 0.020 | 0.229 | |
| omnipath_cache_update_status | 0.221 | 0.022 | 0.285 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_get_config_path | 0.000 | 0.001 | 0.002 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0.001 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.001 | 0.002 | |
| omnipath_msg | 0.013 | 0.001 | 0.017 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.062 | 0.005 | 0.082 | |
| omnipath_set_console_loglevel | 0.003 | 0.001 | 0.004 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.001 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.004 | |
| omnipath_show_db | 0.116 | 0.001 | 0.135 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.001 | |
| only_from | 0.001 | 0.001 | 0.000 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.002 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.004 | |
| ontology_name_id | 0.001 | 0.001 | 0.002 | |
| organism_for | 0.106 | 0.003 | 0.129 | |
| pathwaycommons_download | 0.002 | 0.001 | 0.002 | |
| pivot_annotations | 16.121 | 1.447 | 22.039 | |
| preppi_download | 0.001 | 0.001 | 0.002 | |
| preppi_filter | 0.001 | 0.001 | 0.003 | |
| print_bma_motif_es | 0.306 | 0.037 | 1.236 | |
| print_bma_motif_vs | 0.249 | 0.016 | 0.798 | |
| print_interactions | 12.791 | 0.399 | 16.702 | |
| print_path_es | 0.845 | 0.057 | 2.208 | |
| print_path_vs | 4.405 | 0.109 | 7.136 | |
| pubmed_open | 10.188 | 0.307 | 12.630 | |
| query_info | 0.160 | 0.016 | 0.747 | |
| ramilowski_download | 0.001 | 0.002 | 0.003 | |
| regnetwork_directions | 0.001 | 0.001 | 0.002 | |
| regnetwork_download | 0.001 | 0.001 | 0.002 | |
| relations_list_to_table | 0.168 | 0.006 | 0.202 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.001 | |
| relations_table_to_list | 0.131 | 0.008 | 0.195 | |
| remap_dorothea_download | 0.001 | 0.001 | 0.002 | |
| remap_filtered | 0.000 | 0.001 | 0.002 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.001 | |
| resource_info | 0.291 | 0.128 | 0.957 | |
| resources_colname | 0.889 | 0.090 | 1.895 | |
| resources_in | 8.993 | 0.058 | 10.674 | |
| show_network | 0.000 | 0.000 | 0.001 | |
| simplify_intercell_network | 0.002 | 0.001 | 0.002 | |
| static_table | 9.486 | 0.746 | 11.942 | |
| static_tables | 0.095 | 0.002 | 0.197 | |
| swap_relations | 0.141 | 0.005 | 0.164 | |
| swissprots_only | 0.123 | 0.004 | 0.140 | |
| tfcensus_download | 0.304 | 0.025 | 0.443 | |
| translate_ids | 0.002 | 0.000 | 0.004 | |
| trembls_only | 0.055 | 0.001 | 0.064 | |
| trrust_download | 0.001 | 0.001 | 0.002 | |
| uniprot_full_id_mapping_table | 0.002 | 0.001 | 0.003 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.004 | |
| uniprot_id_type | 0.004 | 0.001 | 0.005 | |
| uniprot_idmapping_id_types | 0.298 | 0.015 | 0.959 | |
| unique_intercell_network | 0.001 | 0.001 | 0.002 | |
| unnest_evidences | 0.000 | 0.001 | 0.001 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.005 | |
| vinayagam_download | 0.001 | 0.001 | 0.002 | |
| walk_ontology_tree | 0.002 | 0.001 | 0.003 | |
| with_extra_attrs | 21.450 | 0.367 | 25.673 | |
| with_references | 0.759 | 0.051 | 1.847 | |
| zenodo_download | 0.002 | 0.001 | 0.004 | |