Denes Turei
| Snapshot Date: 2024-10-17 13:40 -0400 (Thu, 17 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: 646d054 |
| git_last_commit_date: 2024-10-15 11:12:02 -0400 (Tue, 15 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-18 11:44 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4474 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4733 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4509 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| 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 1446/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.13.28 (landing page) Denes Turei
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 3.13.28 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.28.tar.gz |
| StartedAt: 2024-10-18 04:53:13 -0400 (Fri, 18 Oct 2024) |
| EndedAt: 2024-10-18 05:25:23 -0400 (Fri, 18 Oct 2024) |
| EllapsedTime: 1929.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.28.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: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.28’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-18 04:57:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:17] [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
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 04:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 04:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-18 04:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-18 04:57:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-18 04:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-18 04:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 04:57:29] [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 76.382 0.078 78.077
curated_ligrec_stats 31.092 1.418 105.235
omnipath-interactions 20.975 0.895 48.283
pivot_annotations 14.704 0.827 27.077
filter_extra_attrs 14.672 0.086 15.323
translate_ids_multi 11.434 0.624 29.582
print_interactions 9.707 0.208 16.195
go_annot_download 8.841 0.570 9.626
extra_attr_values 9.000 0.296 11.876
omnipath_for_cosmos 8.853 0.124 80.742
nichenet_gr_network_omnipath 8.456 0.253 11.009
with_extra_attrs 8.155 0.386 11.520
extra_attrs_to_cols 7.832 0.120 7.952
giant_component 7.551 0.393 10.554
pubmed_open 7.207 0.218 9.314
resources_in 7.047 0.119 8.936
nichenet_signaling_network_omnipath 7.011 0.137 9.670
omnipath_query 6.894 0.095 8.043
filter_intercell 6.031 0.486 10.601
static_table 5.297 0.335 11.281
signed_ptms 5.199 0.096 5.941
extra_attrs 5.106 0.133 5.240
curated_ligand_receptor_interactions 4.514 0.440 15.322
filter_by_resource 4.310 0.169 6.764
translate_ids 2.474 0.139 21.234
print_path_vs 2.331 0.208 5.253
uniprot_full_id_mapping_table 1.893 0.092 137.358
ensembl_id_mapping_table 1.110 0.053 76.550
all_uniprots 0.948 0.151 23.016
biomart_query 0.800 0.081 9.080
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Contains 8 files. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 15:34:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:10] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 15:34:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 15:34:12] [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-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)
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Contains 21 files.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-18 05:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-18 05:12:57] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
16.330 1.183 47.942
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.016 | 0.012 | 0.028 | |
| all_uniprots | 0.948 | 0.151 | 23.016 | |
| ancestors | 0.010 | 0.002 | 0.011 | |
| annotated_network | 0.845 | 0.196 | 4.449 | |
| annotation_categories | 76.382 | 0.078 | 78.077 | |
| annotation_resources | 0.129 | 0.019 | 1.009 | |
| annotations | 0.348 | 0.056 | 1.335 | |
| biomart_query | 0.800 | 0.081 | 9.080 | |
| bioplex1 | 0.010 | 0.001 | 0.011 | |
| bioplex2 | 0.011 | 0.000 | 0.011 | |
| bioplex3 | 0.01 | 0.00 | 0.01 | |
| bioplex_all | 0.01 | 0.00 | 0.01 | |
| bioplex_hct116_1 | 0.01 | 0.00 | 0.01 | |
| bma_motif_es | 0.405 | 0.053 | 1.174 | |
| bma_motif_vs | 0.229 | 0.003 | 0.800 | |
| chalmers_gem | 0.010 | 0.002 | 0.010 | |
| chalmers_gem_id_mapping_table | 0.01 | 0.00 | 0.01 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.01 | 0.00 | 0.01 | |
| chalmers_gem_network | 0.010 | 0.000 | 0.011 | |
| chalmers_gem_raw | 0.009 | 0.001 | 0.010 | |
| chalmers_gem_reactions | 0.009 | 0.001 | 0.010 | |
| common_name | 0.028 | 0.000 | 0.028 | |
| complex_genes | 0.537 | 0.015 | 2.133 | |
| complex_resources | 0.132 | 0.026 | 0.888 | |
| complexes | 0.234 | 0.043 | 0.956 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.010 | 0.001 | 0.010 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 4.514 | 0.440 | 15.322 | |
| curated_ligrec_stats | 31.092 | 1.418 | 105.235 | |
| database_summary | 1.363 | 0.072 | 3.735 | |
| descendants | 0.011 | 0.000 | 0.011 | |
| ensembl_dataset | 0.008 | 0.001 | 0.010 | |
| ensembl_id_mapping_table | 1.110 | 0.053 | 76.550 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.078 | 0.000 | 0.078 | |
| ensembl_organisms | 0.099 | 0.001 | 0.100 | |
| ensembl_organisms_raw | 0.119 | 0.001 | 0.119 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 1.777 | 0.034 | 4.610 | |
| enzsub_resources | 0.127 | 0.001 | 0.873 | |
| enzyme_substrate | 1.095 | 0.011 | 1.747 | |
| evex_download | 0.009 | 0.000 | 0.009 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 9.000 | 0.296 | 11.876 | |
| extra_attrs | 5.106 | 0.133 | 5.240 | |
| extra_attrs_to_cols | 7.832 | 0.120 | 7.952 | |
| filter_by_resource | 4.310 | 0.169 | 6.764 | |
| filter_extra_attrs | 14.672 | 0.086 | 15.323 | |
| filter_intercell | 6.031 | 0.486 | 10.601 | |
| filter_intercell_network | 0.021 | 0.002 | 0.023 | |
| find_all_paths | 4.462 | 0.171 | 4.633 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.011 | 0.000 | 0.010 | |
| giant_component | 7.551 | 0.393 | 10.554 | |
| go_annot_download | 8.841 | 0.570 | 9.626 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.009 | 0.001 | 0.009 | |
| guide2pharma_download | 0.010 | 0.000 | 0.009 | |
| harmonizome_download | 0.008 | 0.001 | 0.009 | |
| has_extra_attrs | 4.854 | 0.097 | 4.951 | |
| hmdb_id_mapping_table | 0.01 | 0.00 | 0.01 | |
| hmdb_id_type | 0.002 | 0.000 | 0.002 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.009 | 0.000 | 0.010 | |
| homologene_download | 0.009 | 0.000 | 0.009 | |
| homologene_raw | 0.019 | 0.000 | 0.019 | |
| homologene_uniprot_orthology | 0.01 | 0.00 | 0.01 | |
| hpo_download | 1.726 | 0.130 | 2.441 | |
| htridb_download | 0.010 | 0.001 | 0.011 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.036 | 0.000 | 0.037 | |
| inbiomap_download | 0.001 | 0.000 | 0.000 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.291 | 0.025 | 0.770 | |
| interaction_graph | 0.316 | 0.007 | 0.967 | |
| interaction_resources | 0.081 | 0.003 | 0.855 | |
| interaction_types | 0.040 | 0.001 | 0.041 | |
| intercell | 0.352 | 0.047 | 0.875 | |
| intercell_categories | 0.317 | 0.035 | 0.557 | |
| intercell_consensus_filter | 1.008 | 0.085 | 3.072 | |
| intercell_generic_categories | 0.044 | 0.000 | 0.044 | |
| intercell_network | 0.009 | 0.001 | 0.009 | |
| intercell_resources | 0.084 | 0.001 | 0.831 | |
| intercell_summary | 0.045 | 0.002 | 0.047 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.027 | 0.001 | 0.028 | |
| is_trembl | 0.048 | 0.001 | 0.051 | |
| is_uniprot | 0.011 | 0.000 | 0.010 | |
| kegg_info | 0.010 | 0.000 | 0.009 | |
| kegg_open | 0.010 | 0.000 | 0.009 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.01 | 0.00 | 0.01 | |
| kegg_pathway_list | 0.009 | 0.001 | 0.009 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 0.156 | 0.004 | 4.444 | |
| kegg_process | 0.042 | 0.000 | 0.043 | |
| latin_name | 0.056 | 0.000 | 0.056 | |
| load_db | 0.062 | 0.001 | 0.063 | |
| ncbi_taxid | 0.049 | 0.000 | 0.050 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.010 | 0.000 | 0.011 | |
| nichenet_gr_network | 0.025 | 0.001 | 0.027 | |
| nichenet_gr_network_evex | 0.009 | 0.000 | 0.010 | |
| nichenet_gr_network_harmonizome | 0.031 | 0.001 | 0.031 | |
| nichenet_gr_network_htridb | 0.010 | 0.000 | 0.009 | |
| nichenet_gr_network_omnipath | 8.456 | 0.253 | 11.009 | |
| nichenet_gr_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0.009 | 0.000 | 0.009 | |
| nichenet_gr_network_remap | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_trrust | 0.009 | 0.000 | 0.009 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0.000 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.026 | 0.001 | 0.027 | |
| nichenet_lr_network_guide2pharma | 0.009 | 0.000 | 0.009 | |
| nichenet_lr_network_omnipath | 0.047 | 0.003 | 0.049 | |
| nichenet_lr_network_ramilowski | 0.009 | 0.000 | 0.009 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.044 | 0.000 | 0.044 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.027 | 0.000 | 0.028 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.028 | 0.000 | 0.028 | |
| nichenet_signaling_network_cpdb | 0.009 | 0.000 | 0.009 | |
| nichenet_signaling_network_evex | 0.009 | 0.000 | 0.009 | |
| nichenet_signaling_network_harmonizome | 0.01 | 0.00 | 0.01 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 7.011 | 0.137 | 9.670 | |
| nichenet_signaling_network_pathwaycommons | 0.013 | 0.000 | 0.013 | |
| nichenet_signaling_network_vinayagam | 0.013 | 0.000 | 0.012 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.083 | 0.001 | 0.137 | |
| oma_code | 0.026 | 0.000 | 0.026 | |
| oma_organisms | 0.046 | 0.002 | 0.048 | |
| oma_pairwise | 0.010 | 0.000 | 0.011 | |
| oma_pairwise_genesymbols | 0.009 | 0.001 | 0.010 | |
| oma_pairwise_translated | 0.01 | 0.00 | 0.01 | |
| omnipath-interactions | 20.975 | 0.895 | 48.283 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.005 | 0.000 | 0.005 | |
| omnipath_cache_clean_db | 0.070 | 0.003 | 0.074 | |
| omnipath_cache_download_ready | 0.437 | 0.018 | 0.478 | |
| omnipath_cache_filter_versions | 0.090 | 0.004 | 0.114 | |
| omnipath_cache_get | 0.077 | 0.004 | 0.081 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_latest_or_new | 0.057 | 0.002 | 0.059 | |
| omnipath_cache_load | 0.786 | 0.017 | 3.757 | |
| omnipath_cache_move_in | 0.164 | 0.003 | 0.170 | |
| omnipath_cache_remove | 0.094 | 0.003 | 0.100 | |
| omnipath_cache_save | 0.193 | 0.006 | 0.308 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.067 | 0.008 | 0.078 | |
| omnipath_cache_update_status | 0.084 | 0.003 | 0.087 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 8.853 | 0.124 | 80.742 | |
| omnipath_load_config | 0.001 | 0.000 | 0.000 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.002 | 0.000 | 0.003 | |
| omnipath_msg | 0.011 | 0.000 | 0.012 | |
| omnipath_query | 6.894 | 0.095 | 8.043 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.070 | 0.006 | 0.076 | |
| omnipath_set_console_loglevel | 0.007 | 0.000 | 0.007 | |
| omnipath_set_logfile_loglevel | 0.145 | 0.000 | 0.145 | |
| omnipath_set_loglevel | 0.004 | 0.000 | 0.004 | |
| omnipath_show_db | 0.148 | 0.002 | 0.150 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.001 | 0.001 | |
| ontology_name_id | 0.001 | 0.001 | 0.001 | |
| organism_for | 0.112 | 0.000 | 0.112 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 14.704 | 0.827 | 27.077 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.002 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.523 | 0.043 | 1.657 | |
| print_bma_motif_vs | 0.247 | 0.004 | 1.011 | |
| print_interactions | 9.707 | 0.208 | 16.195 | |
| print_path_es | 0.829 | 0.092 | 2.700 | |
| print_path_vs | 2.331 | 0.208 | 5.253 | |
| pubmed_open | 7.207 | 0.218 | 9.314 | |
| query_info | 0.240 | 0.006 | 0.642 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.004 | 0.000 | 0.011 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.000 | |
| ramp_tables | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.243 | 0.001 | 0.547 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.004 | |
| relations_table_to_list | 0.186 | 0.003 | 0.393 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.002 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.372 | 0.020 | 1.112 | |
| resources | 0.181 | 0.036 | 1.009 | |
| resources_colname | 0.994 | 0.062 | 3.189 | |
| resources_in | 7.047 | 0.119 | 8.936 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.199 | 0.096 | 5.941 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.002 | |
| static_table | 5.297 | 0.335 | 11.281 | |
| static_tables | 0.043 | 0.000 | 0.050 | |
| stitch_actions | 0.001 | 0.000 | 0.000 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0.006 | 0.000 | 0.007 | |
| swap_relations | 0.102 | 0.000 | 0.120 | |
| swissprots_only | 0.028 | 0.000 | 0.029 | |
| tfcensus_download | 0.196 | 0.005 | 0.345 | |
| translate_ids | 2.474 | 0.139 | 21.234 | |
| translate_ids_multi | 11.434 | 0.624 | 29.582 | |
| trembls_only | 0.072 | 0.000 | 0.072 | |
| trrust_download | 0.001 | 0.000 | 0.002 | |
| uniprot_full_id_mapping_table | 1.893 | 0.092 | 137.358 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.000 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.002 | |
| uniprot_id_type | 0.004 | 0.000 | 0.004 | |
| uniprot_idmapping_id_types | 0.344 | 0.010 | 0.881 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.004 | 0.000 | 0.004 | |
| vinayagam_download | 0.001 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.002 | 0.000 | 0.002 | |
| with_extra_attrs | 8.155 | 0.386 | 11.520 | |
| with_references | 0.489 | 0.043 | 2.181 | |
| zenodo_download | 0.002 | 0.000 | 0.002 | |