Denes Turei
| Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 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" | 4505 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| teran2 | 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 | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| 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: 3.14.0 |
| 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_3.14.0.tar.gz |
| StartedAt: 2024-11-09 08:58:44 -0500 (Sat, 09 Nov 2024) |
| EndedAt: 2024-11-09 09:10:05 -0500 (Sat, 09 Nov 2024) |
| EllapsedTime: 680.6 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_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...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 whether startup messages can be suppressed ... NOTE
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [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 34.389 0.022 35.994
curated_ligrec_stats 8.123 0.373 71.706
omnipath-interactions 7.892 0.285 32.651
filter_extra_attrs 5.154 0.023 5.750
pivot_annotations 3.950 0.222 13.445
nichenet_gr_network_omnipath 3.704 0.292 6.296
extra_attr_values 3.238 0.051 5.885
giant_component 2.913 0.107 5.818
with_extra_attrs 2.808 0.069 5.688
translate_ids_multi 2.769 0.060 15.591
nichenet_signaling_network_omnipath 2.647 0.147 5.486
omnipath_for_cosmos 2.646 0.063 18.125
static_table 2.264 0.112 8.425
filter_intercell 2.073 0.121 6.968
print_interactions 1.732 0.045 6.323
curated_ligand_receptor_interactions 1.295 0.077 10.834
ensembl_id_mapping_table 0.683 0.021 15.998
translate_ids 0.390 0.036 17.199
uniprot_full_id_mapping_table 0.336 0.089 21.063
all_uniprots 0.231 0.020 19.108
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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-arm64/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 [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Contains 1 files. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-08 15:34:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:34:59] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Contains 1 files. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-08 15:35:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-08 15:35:00] [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: aarch64-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)
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Contains 21 files.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 09:09:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:09:28] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
3.534 0.385 30.754
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.004 | 0.000 | 0.005 | |
| all_uniprots | 0.231 | 0.020 | 19.108 | |
| ancestors | 0.002 | 0.000 | 0.003 | |
| annotated_network | 0.210 | 0.019 | 3.396 | |
| annotation_categories | 34.389 | 0.022 | 35.994 | |
| annotation_resources | 0.017 | 0.002 | 0.698 | |
| annotations | 0.061 | 0.005 | 0.799 | |
| biomart_query | 0.445 | 0.018 | 2.819 | |
| bioplex1 | 0.002 | 0.001 | 0.002 | |
| bioplex2 | 0.001 | 0.000 | 0.002 | |
| bioplex3 | 0.001 | 0.000 | 0.002 | |
| bioplex_all | 0.002 | 0.000 | 0.002 | |
| bioplex_hct116_1 | 0.003 | 0.001 | 0.003 | |
| bma_motif_es | 0.106 | 0.009 | 0.910 | |
| bma_motif_vs | 0.055 | 0.003 | 0.629 | |
| chalmers_gem | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_id_mapping_table | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.002 | 0.001 | 0.002 | |
| chalmers_gem_network | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_raw | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_reactions | 0.001 | 0.000 | 0.002 | |
| common_name | 0.008 | 0.000 | 0.009 | |
| complex_genes | 0.147 | 0.008 | 1.875 | |
| complex_resources | 0.017 | 0.001 | 0.551 | |
| complexes | 0.049 | 0.002 | 0.584 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.002 | 0.000 | 0.002 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 1.295 | 0.077 | 10.834 | |
| curated_ligrec_stats | 8.123 | 0.373 | 71.706 | |
| database_summary | 0.420 | 0.010 | 2.832 | |
| descendants | 0.002 | 0.000 | 0.003 | |
| ensembl_dataset | 0.004 | 0.000 | 0.004 | |
| ensembl_id_mapping_table | 0.683 | 0.021 | 15.998 | |
| ensembl_id_type | 0.001 | 0.000 | 0.001 | |
| ensembl_name | 0.014 | 0.000 | 0.015 | |
| ensembl_organisms | 0.032 | 0.001 | 0.033 | |
| ensembl_organisms_raw | 0.056 | 0.001 | 0.058 | |
| ensembl_orthology | 0.000 | 0.001 | 0.000 | |
| enzsub_graph | 0.642 | 0.017 | 2.468 | |
| enzsub_resources | 0.016 | 0.001 | 0.612 | |
| enzyme_substrate | 0.280 | 0.005 | 0.856 | |
| evex_download | 0.002 | 0.000 | 0.003 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 3.238 | 0.051 | 5.885 | |
| extra_attrs | 1.849 | 0.012 | 1.861 | |
| extra_attrs_to_cols | 2.72 | 0.02 | 2.74 | |
| filter_by_resource | 1.639 | 0.032 | 3.856 | |
| filter_extra_attrs | 5.154 | 0.023 | 5.750 | |
| filter_intercell | 2.073 | 0.121 | 6.968 | |
| filter_intercell_network | 0.004 | 0.001 | 0.004 | |
| find_all_paths | 1.470 | 0.032 | 1.502 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.002 | 0.000 | 0.002 | |
| giant_component | 2.913 | 0.107 | 5.818 | |
| go_annot_download | 4.057 | 0.172 | 4.207 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.002 | 0.000 | 0.002 | |
| guide2pharma_download | 0.002 | 0.001 | 0.002 | |
| harmonizome_download | 0.002 | 0.000 | 0.002 | |
| has_extra_attrs | 1.804 | 0.018 | 1.822 | |
| hmdb_id_mapping_table | 0.002 | 0.000 | 0.002 | |
| hmdb_id_type | 0.001 | 0.000 | 0.000 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.000 | |
| hmdb_table | 0.002 | 0.000 | 0.003 | |
| homologene_download | 0.003 | 0.000 | 0.002 | |
| homologene_raw | 0.005 | 0.000 | 0.006 | |
| homologene_uniprot_orthology | 0.002 | 0.001 | 0.003 | |
| hpo_download | 0.832 | 0.048 | 1.298 | |
| htridb_download | 0.002 | 0.001 | 0.003 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.011 | 0.000 | 0.011 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.093 | 0.007 | 0.349 | |
| interaction_graph | 0.122 | 0.002 | 0.723 | |
| interaction_resources | 0.021 | 0.002 | 0.630 | |
| interaction_types | 0.011 | 0.000 | 0.012 | |
| intercell | 0.111 | 0.010 | 0.719 | |
| intercell_categories | 0.092 | 0.008 | 0.327 | |
| intercell_consensus_filter | 0.398 | 0.025 | 2.244 | |
| intercell_generic_categories | 0.013 | 0.000 | 0.013 | |
| intercell_network | 0.002 | 0.001 | 0.003 | |
| intercell_resources | 0.020 | 0.001 | 0.621 | |
| intercell_summary | 0.013 | 0.003 | 0.017 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.007 | 0.000 | 0.007 | |
| is_trembl | 0.007 | 0.000 | 0.008 | |
| is_uniprot | 0.003 | 0.000 | 0.002 | |
| kegg_info | 0.002 | 0.000 | 0.002 | |
| kegg_open | 0.002 | 0.000 | 0.002 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.002 | 0.000 | 0.003 | |
| kegg_pathway_list | 0.013 | 0.002 | 0.013 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.019 | 0.003 | 4.504 | |
| kegg_process | 0.004 | 0.000 | 0.004 | |
| latin_name | 0.015 | 0.000 | 0.015 | |
| load_db | 0.019 | 0.000 | 0.020 | |
| ncbi_taxid | 0.015 | 0.001 | 0.015 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network | 0.006 | 0.001 | 0.007 | |
| nichenet_gr_network_evex | 0.002 | 0.000 | 0.002 | |
| nichenet_gr_network_harmonizome | 0.002 | 0.000 | 0.003 | |
| nichenet_gr_network_htridb | 0.002 | 0.000 | 0.002 | |
| nichenet_gr_network_omnipath | 3.704 | 0.292 | 6.296 | |
| nichenet_gr_network_pathwaycommons | 0.002 | 0.000 | 0.002 | |
| nichenet_gr_network_regnetwork | 0.002 | 0.000 | 0.002 | |
| nichenet_gr_network_remap | 0.002 | 0.001 | 0.002 | |
| nichenet_gr_network_trrust | 0.002 | 0.000 | 0.002 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.014 | 0.000 | 0.014 | |
| nichenet_lr_network_guide2pharma | 0.002 | 0.001 | 0.002 | |
| nichenet_lr_network_omnipath | 0.005 | 0.000 | 0.005 | |
| nichenet_lr_network_ramilowski | 0.002 | 0.000 | 0.002 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.008 | 0.001 | 0.009 | |
| nichenet_optimization | 0.000 | 0.000 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.005 | 0.000 | 0.005 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.005 | 0.000 | 0.006 | |
| nichenet_signaling_network_cpdb | 0.002 | 0.001 | 0.001 | |
| nichenet_signaling_network_evex | 0.002 | 0.000 | 0.001 | |
| nichenet_signaling_network_harmonizome | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 2.647 | 0.147 | 5.486 | |
| nichenet_signaling_network_pathwaycommons | 0.002 | 0.001 | 0.002 | |
| nichenet_signaling_network_vinayagam | 0.002 | 0.000 | 0.003 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.028 | 0.002 | 0.075 | |
| oma_code | 0.008 | 0.000 | 0.008 | |
| oma_organisms | 0.015 | 0.001 | 0.015 | |
| oma_pairwise | 0.002 | 0.000 | 0.002 | |
| oma_pairwise_genesymbols | 0.002 | 0.000 | 0.003 | |
| oma_pairwise_translated | 0.003 | 0.000 | 0.002 | |
| omnipath-interactions | 7.892 | 0.285 | 32.651 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.001 | 0.000 | 0.002 | |
| omnipath_cache_clean_db | 0.031 | 0.002 | 0.033 | |
| omnipath_cache_download_ready | 0.111 | 0.010 | 0.152 | |
| omnipath_cache_filter_versions | 0.021 | 0.002 | 0.073 | |
| omnipath_cache_get | 0.019 | 0.003 | 0.021 | |
| omnipath_cache_key | 0 | 0 | 0 | |
| omnipath_cache_latest_or_new | 0.013 | 0.002 | 0.015 | |
| omnipath_cache_load | 0.187 | 0.009 | 2.668 | |
| omnipath_cache_move_in | 0.030 | 0.004 | 0.038 | |
| omnipath_cache_remove | 0.019 | 0.003 | 0.024 | |
| omnipath_cache_save | 0.032 | 0.004 | 0.053 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.018 | 0.002 | 0.024 | |
| omnipath_cache_update_status | 0.028 | 0.002 | 0.031 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.000 | 0.001 | 0.000 | |
| omnipath_for_cosmos | 2.646 | 0.063 | 18.125 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.000 | 0.000 | |
| omnipath_msg | 0.001 | 0.001 | 0.001 | |
| omnipath_query | 1.197 | 0.011 | 1.210 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.007 | 0.001 | 0.007 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.014 | 0.001 | 0.015 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.000 | |
| organism_for | 0.025 | 0.000 | 0.026 | |
| pathwaycommons_download | 0.001 | 0.001 | 0.001 | |
| pivot_annotations | 3.950 | 0.222 | 13.445 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.056 | 0.009 | 0.849 | |
| print_bma_motif_vs | 0.033 | 0.002 | 0.670 | |
| print_interactions | 1.732 | 0.045 | 6.323 | |
| print_path_es | 0.151 | 0.012 | 1.736 | |
| print_path_vs | 0.652 | 0.018 | 3.170 | |
| pubmed_open | 1.280 | 0.025 | 1.306 | |
| query_info | 0.024 | 0.003 | 0.244 | |
| ramilowski_download | 0.000 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0.001 | 0.000 | 0.001 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.000 | 0.001 | 0.000 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0.000 | 0.000 | 0.001 | |
| relations_list_to_table | 0.020 | 0.001 | 0.034 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.016 | 0.004 | 0.135 | |
| remap_dorothea_download | 0.000 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.039 | 0.014 | 0.646 | |
| resources | 0.015 | 0.003 | 0.642 | |
| resources_colname | 0.213 | 0.012 | 2.284 | |
| resources_in | 0.902 | 0.015 | 0.917 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 1.207 | 0.011 | 1.788 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 2.264 | 0.112 | 8.425 | |
| static_tables | 0.043 | 0.002 | 0.050 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0.002 | 0.000 | 0.002 | |
| swap_relations | 0.020 | 0.002 | 0.036 | |
| swissprots_only | 0.009 | 0.000 | 0.009 | |
| tfcensus_download | 0.047 | 0.004 | 0.219 | |
| translate_ids | 0.390 | 0.036 | 17.199 | |
| translate_ids_multi | 2.769 | 0.060 | 15.591 | |
| trembls_only | 0.007 | 0.000 | 0.008 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 0.336 | 0.089 | 21.063 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.000 | 0.001 | |
| uniprot_idmapping_id_types | 0.053 | 0.009 | 0.457 | |
| unique_intercell_network | 0 | 0 | 0 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.001 | 0.000 | 0.001 | |
| vinayagam_download | 0.000 | 0.001 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.000 | |
| with_extra_attrs | 2.808 | 0.069 | 5.688 | |
| with_references | 0.134 | 0.017 | 1.461 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |