Denes Turei
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: bc4d2dd |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:40 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 1449/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.15.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 3.15.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz |
| StartedAt: 2025-01-04 00:36:05 -0500 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 01:01:30 -0500 (Sat, 04 Jan 2025) |
| EllapsedTime: 1524.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 00:36:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:29] [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
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:36:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:36:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-04 00:36:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 00:36:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 00:36:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 00:36:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 00:36:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:36:42] [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 85.397 0.050 87.119
omnipath-interactions 45.412 1.996 96.301
curated_ligrec_stats 29.750 1.462 108.074
nichenet_signaling_network_omnipath 18.131 0.163 28.541
pivot_annotations 15.604 1.072 38.316
filter_extra_attrs 15.637 0.144 16.471
nichenet_gr_network_omnipath 12.360 0.168 14.534
omnipath_for_cosmos 10.261 0.255 23.629
print_interactions 9.784 0.632 18.452
extra_attr_values 9.744 0.354 14.947
translate_ids_multi 9.791 0.266 19.951
go_annot_download 9.406 0.472 10.155
static_table 8.943 0.755 13.679
extra_attrs_to_cols 9.310 0.041 9.351
with_extra_attrs 8.738 0.113 11.499
giant_component 8.619 0.180 13.843
signed_ptms 8.417 0.161 19.219
omnipath_query 8.101 0.105 14.101
filter_by_resource 6.102 0.214 8.776
resources_in 6.010 0.292 12.458
has_extra_attrs 5.458 0.013 5.471
filter_intercell 5.111 0.285 9.259
extra_attrs 5.250 0.077 5.327
curated_ligand_receptor_interactions 4.507 0.244 17.139
pubmed_open 4.564 0.101 5.141
print_path_vs 2.722 0.119 5.386
translate_ids 2.174 0.048 21.356
ensembl_id_mapping_table 1.214 0.075 10.350
uniprot_full_id_mapping_table 1.185 0.027 22.257
all_uniprots 0.895 0.071 20.216
* 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-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-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 [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Contains 8 files. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 15:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:05] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Contains 1 files. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 15:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 15:30:07] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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)
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:50:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Contains 21 files.
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 00:50:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 00:50:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 00:50:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 00:50:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 00:50:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 00:50:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 00:50:07] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
14.442 1.527 59.242
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.000 | 0.000 | |
| all_uniprot_acs | 0.016 | 0.004 | 0.018 | |
| all_uniprots | 0.895 | 0.071 | 20.216 | |
| ancestors | 0.005 | 0.004 | 0.010 | |
| annotated_network | 0.840 | 0.100 | 4.369 | |
| annotation_categories | 85.397 | 0.050 | 87.119 | |
| annotation_resources | 0.129 | 0.011 | 0.926 | |
| annotations | 0.343 | 0.024 | 1.358 | |
| biomart_query | 0.712 | 0.034 | 3.782 | |
| bioplex1 | 0.007 | 0.001 | 0.008 | |
| bioplex2 | 0.006 | 0.001 | 0.008 | |
| bioplex3 | 0.007 | 0.001 | 0.008 | |
| bioplex_all | 0.039 | 0.001 | 0.040 | |
| bioplex_hct116_1 | 0.009 | 0.000 | 0.009 | |
| bma_motif_es | 0.335 | 0.065 | 1.526 | |
| bma_motif_vs | 0.248 | 0.005 | 0.858 | |
| chalmers_gem | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.000 | 0.007 | |
| chalmers_gem_network | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_raw | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_reactions | 0.007 | 0.000 | 0.007 | |
| common_name | 0.028 | 0.000 | 0.028 | |
| complex_genes | 0.522 | 0.018 | 2.370 | |
| complex_resources | 0.139 | 0.003 | 0.743 | |
| complexes | 0.220 | 0.002 | 0.889 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.006 | 0.001 | 0.007 | |
| cosmos_pkn | 0.001 | 0.000 | 0.000 | |
| curated_ligand_receptor_interactions | 4.507 | 0.244 | 17.139 | |
| curated_ligrec_stats | 29.750 | 1.462 | 108.074 | |
| database_summary | 1.326 | 0.054 | 4.149 | |
| descendants | 0.01 | 0.00 | 0.01 | |
| ensembl_dataset | 0.010 | 0.001 | 0.011 | |
| ensembl_id_mapping_table | 1.214 | 0.075 | 10.350 | |
| ensembl_id_type | 0.003 | 0.000 | 0.003 | |
| ensembl_name | 0.060 | 0.006 | 0.065 | |
| ensembl_organisms | 0.131 | 0.018 | 0.149 | |
| ensembl_organisms_raw | 0.104 | 0.002 | 0.107 | |
| ensembl_orthology | 0.001 | 0.000 | 0.001 | |
| enzsub_graph | 1.854 | 0.073 | 4.632 | |
| enzsub_resources | 0.085 | 0.005 | 0.654 | |
| enzyme_substrate | 1.133 | 0.045 | 1.943 | |
| evex_download | 0.007 | 0.001 | 0.008 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 9.744 | 0.354 | 14.947 | |
| extra_attrs | 5.250 | 0.077 | 5.327 | |
| extra_attrs_to_cols | 9.310 | 0.041 | 9.351 | |
| filter_by_resource | 6.102 | 0.214 | 8.776 | |
| filter_extra_attrs | 15.637 | 0.144 | 16.471 | |
| filter_intercell | 5.111 | 0.285 | 9.259 | |
| filter_intercell_network | 0.017 | 0.001 | 0.018 | |
| find_all_paths | 4.619 | 0.067 | 4.686 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.007 | 0.002 | 0.009 | |
| giant_component | 8.619 | 0.180 | 13.843 | |
| go_annot_download | 9.406 | 0.472 | 10.155 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.006 | 0.002 | 0.009 | |
| guide2pharma_download | 0.008 | 0.000 | 0.008 | |
| harmonizome_download | 0.008 | 0.000 | 0.008 | |
| has_extra_attrs | 5.458 | 0.013 | 5.471 | |
| hmdb_id_mapping_table | 0.008 | 0.000 | 0.009 | |
| hmdb_id_type | 0.000 | 0.002 | 0.002 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_table | 0.006 | 0.002 | 0.008 | |
| homologene_download | 0.008 | 0.000 | 0.008 | |
| homologene_raw | 0.017 | 0.001 | 0.018 | |
| homologene_uniprot_orthology | 0.008 | 0.000 | 0.008 | |
| hpo_download | 1.884 | 0.098 | 2.431 | |
| htridb_download | 0.01 | 0.00 | 0.01 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.037 | 0.000 | 0.037 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.324 | 0.006 | 0.612 | |
| interaction_graph | 0.375 | 0.004 | 0.943 | |
| interaction_resources | 0.116 | 0.005 | 0.674 | |
| interaction_types | 0.037 | 0.000 | 0.037 | |
| intercell | 0.390 | 0.042 | 0.992 | |
| intercell_categories | 0.322 | 0.018 | 0.527 | |
| intercell_consensus_filter | 0.992 | 0.066 | 3.031 | |
| intercell_generic_categories | 0.043 | 0.001 | 0.043 | |
| intercell_network | 0.008 | 0.000 | 0.008 | |
| intercell_resources | 0.121 | 0.005 | 0.793 | |
| intercell_summary | 0.041 | 0.015 | 0.057 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.025 | 0.003 | 0.028 | |
| is_trembl | 0.025 | 0.001 | 0.026 | |
| is_uniprot | 0.008 | 0.001 | 0.009 | |
| kegg_info | 0.007 | 0.001 | 0.007 | |
| kegg_open | 0.007 | 0.001 | 0.007 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.000 | |
| kegg_pathway_download | 0.007 | 0.001 | 0.008 | |
| kegg_pathway_list | 0.007 | 0.000 | 0.008 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.210 | 0.006 | 4.756 | |
| kegg_process | 0.015 | 0.000 | 0.016 | |
| latin_name | 0.059 | 0.000 | 0.059 | |
| load_db | 0.065 | 0.000 | 0.066 | |
| ncbi_taxid | 0.055 | 0.001 | 0.056 | |
| nichenet_build_model | 0.001 | 0.000 | 0.000 | |
| nichenet_expression_data | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network | 0.020 | 0.001 | 0.022 | |
| nichenet_gr_network_evex | 0.006 | 0.001 | 0.007 | |
| nichenet_gr_network_harmonizome | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_htridb | 0.004 | 0.003 | 0.007 | |
| nichenet_gr_network_omnipath | 12.360 | 0.168 | 14.534 | |
| nichenet_gr_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0.006 | 0.002 | 0.008 | |
| nichenet_gr_network_remap | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_trrust | 0.007 | 0.000 | 0.008 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.022 | 0.000 | 0.022 | |
| nichenet_lr_network_guide2pharma | 0.007 | 0.001 | 0.007 | |
| nichenet_lr_network_omnipath | 0.021 | 0.002 | 0.022 | |
| nichenet_lr_network_ramilowski | 0.007 | 0.001 | 0.008 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.035 | 0.003 | 0.038 | |
| nichenet_optimization | 0.000 | 0.000 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.025 | 0.000 | 0.024 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.026 | 0.000 | 0.026 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.001 | 0.009 | |
| nichenet_signaling_network_evex | 0.008 | 0.000 | 0.009 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_inbiomap | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network_omnipath | 18.131 | 0.163 | 28.541 | |
| nichenet_signaling_network_pathwaycommons | 0.026 | 0.001 | 0.057 | |
| nichenet_signaling_network_vinayagam | 0.154 | 0.002 | 0.491 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.000 | 0.000 | 0.001 | |
| obo_parser | 0.211 | 0.003 | 0.502 | |
| oma_code | 0.073 | 0.001 | 0.151 | |
| oma_organisms | 0.113 | 0.002 | 0.233 | |
| oma_pairwise | 0.023 | 0.001 | 0.043 | |
| oma_pairwise_genesymbols | 0.023 | 0.000 | 0.047 | |
| oma_pairwise_translated | 0.021 | 0.001 | 0.041 | |
| omnipath-interactions | 45.412 | 1.996 | 96.301 | |
| omnipath_cache_autoclean | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_clean | 0.005 | 0.001 | 0.007 | |
| omnipath_cache_clean_db | 0.084 | 0.008 | 0.092 | |
| omnipath_cache_download_ready | 0.441 | 0.046 | 0.513 | |
| omnipath_cache_filter_versions | 0.077 | 0.002 | 0.104 | |
| omnipath_cache_get | 0.060 | 0.005 | 0.064 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.042 | 0.005 | 0.047 | |
| omnipath_cache_load | 0.716 | 0.022 | 3.555 | |
| omnipath_cache_move_in | 0.124 | 0.011 | 0.146 | |
| omnipath_cache_remove | 0.078 | 0.006 | 0.094 | |
| omnipath_cache_save | 0.192 | 0.009 | 0.337 | |
| omnipath_cache_search | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.099 | 0.005 | 0.115 | |
| omnipath_cache_update_status | 0.073 | 0.004 | 0.077 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.001 | 0.001 | |
| omnipath_for_cosmos | 10.261 | 0.255 | 23.629 | |
| omnipath_load_config | 0.001 | 0.000 | 0.000 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.001 | 0.003 | |
| omnipath_msg | 0.010 | 0.001 | 0.011 | |
| omnipath_query | 8.101 | 0.105 | 14.101 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0.000 | 0.000 | 0.001 | |
| omnipath_set_cachedir | 0.059 | 0.002 | 0.062 | |
| omnipath_set_console_loglevel | 0.008 | 0.001 | 0.009 | |
| omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.007 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_show_db | 0.314 | 0.000 | 0.444 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.002 | |
| only_from | 0.001 | 0.000 | 0.000 | |
| ontology_ensure_id | 0.001 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.002 | |
| organism_for | 0.125 | 0.002 | 0.128 | |
| pathwaycommons_download | 0.002 | 0.000 | 0.002 | |
| pivot_annotations | 15.604 | 1.072 | 38.316 | |
| preppi_download | 0.000 | 0.002 | 0.002 | |
| preppi_filter | 0.002 | 0.000 | 0.002 | |
| print_bma_motif_es | 0.527 | 0.074 | 1.755 | |
| print_bma_motif_vs | 0.323 | 0.008 | 1.287 | |
| print_interactions | 9.784 | 0.632 | 18.452 | |
| print_path_es | 0.723 | 0.075 | 2.607 | |
| print_path_vs | 2.722 | 0.119 | 5.386 | |
| pubmed_open | 4.564 | 0.101 | 5.141 | |
| query_info | 0.204 | 0.005 | 0.474 | |
| ramilowski_download | 0.001 | 0.001 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.001 | 0.002 | |
| ramp_id_type | 0.004 | 0.000 | 0.004 | |
| 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 | 0.000 | 0.001 | 0.002 | |
| relations_list_to_table | 0.088 | 0.002 | 0.128 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.001 | |
| relations_table_to_list | 0.071 | 0.003 | 0.092 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.199 | 0.058 | 1.119 | |
| resources | 0.122 | 0.003 | 0.738 | |
| resources_colname | 0.838 | 0.080 | 3.147 | |
| resources_in | 6.010 | 0.292 | 12.458 | |
| show_network | 0.000 | 0.000 | 0.001 | |
| signed_ptms | 8.417 | 0.161 | 19.219 | |
| simplify_intercell_network | 0.001 | 0.002 | 0.003 | |
| static_table | 8.943 | 0.755 | 13.679 | |
| static_tables | 0.078 | 0.010 | 0.113 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.001 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.082 | 0.016 | 0.099 | |
| swap_relations | 0.118 | 0.004 | 0.156 | |
| swissprots_only | 0.048 | 0.004 | 0.052 | |
| tfcensus_download | 0.315 | 0.013 | 0.500 | |
| translate_ids | 2.174 | 0.048 | 21.356 | |
| translate_ids_multi | 9.791 | 0.266 | 19.951 | |
| trembls_only | 0.059 | 0.000 | 0.059 | |
| trrust_download | 0.001 | 0.000 | 0.002 | |
| uniprot_full_id_mapping_table | 1.185 | 0.027 | 22.257 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.001 | 0.002 | |
| uniprot_idmapping_id_types | 0.227 | 0.008 | 0.806 | |
| unique_intercell_network | 0.000 | 0.002 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.002 | 0.000 | 0.002 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.002 | 0.000 | 0.002 | |
| with_extra_attrs | 8.738 | 0.113 | 11.499 | |
| with_references | 0.448 | 0.041 | 1.934 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |