| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 1432/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.13.1 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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: 3.13.1 |
| 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_3.13.1.tar.gz |
| StartedAt: 2024-07-23 23:39:52 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 23:47:00 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 428.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_3.13.1.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 ‘3.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 23:40:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:01] [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
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 23:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:40:05] [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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
>
> ### ** Examples
>
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") :
Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
Execution halted
* 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: 1 ERROR, 3 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 [2024-07-23 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Contains 1 files. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:27] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-07-23 15:23:27] [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). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [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). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [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). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [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). [2024-07-23 15:23:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:27] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Contains 1 files. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-23 15:23:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-23 15:23:28] [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)
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 23:46:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-23 23:46:14] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
3.634 0.373 32.591
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.006 | 0.000 | 0.007 | |
| all_uniprots | 0.003 | 0.001 | 0.004 | |
| ancestors | 0.003 | 0.000 | 0.003 | |
| annotated_network | 0.534 | 0.055 | 6.007 | |
| annotation_categories | 35.463 | 0.024 | 37.217 | |
| biomart_query | 0.289 | 0.023 | 7.314 | |
| bioplex1 | 0.004 | 0.000 | 0.004 | |
| bioplex2 | 0.003 | 0.001 | 0.004 | |
| bioplex3 | 0.003 | 0.000 | 0.004 | |
| bioplex_all | 0.003 | 0.001 | 0.004 | |
| bioplex_hct116_1 | 0.003 | 0.000 | 0.004 | |
| bma_motif_es | 0.097 | 0.014 | 1.129 | |
| bma_motif_vs | 0.055 | 0.003 | 0.632 | |
| collectri | 34.486 | 0.147 | 37.495 | |
| common_name | 0.007 | 0.000 | 0.007 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.003 | 0.000 | 0.004 | |
| curated_ligand_receptor_interactions | 1.626 | 0.100 | 13.588 | |
| curated_ligrec_stats | 8.303 | 0.576 | 76.199 | |
| database_summary | 0.397 | 0.019 | 3.407 | |
| descendants | 0.003 | 0.000 | 0.004 | |
| dorothea | 20.071 | 0.097 | 28.281 | |
| ensembl_dataset | 0.007 | 0.000 | 0.007 | |
| ensembl_id_mapping_table | 0.318 | 0.030 | 26.886 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.011 | 0.000 | 0.011 | |
| ensembl_organisms | 0.033 | 0.001 | 0.034 | |
| ensembl_organisms_raw | 0.031 | 0.001 | 0.032 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 0.616 | 0.025 | 3.167 | |
| evex_download | 0.004 | 0.001 | 0.004 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 3.792 | 0.057 | 8.086 | |
| extra_attrs | 2.270 | 0.012 | 2.282 | |
| extra_attrs_to_cols | 2.929 | 0.013 | 2.942 | |
| filter_by_resource | 1.851 | 0.046 | 4.377 | |
| filter_extra_attrs | 5.551 | 0.024 | 6.290 | |
| filter_intercell | 2.387 | 0.127 | 6.749 | |
| filter_intercell_network | 0.006 | 0.001 | 0.008 | |
| find_all_paths | 1.749 | 0.041 | 1.790 | |
| from_evidences | 0 | 0 | 0 | |
| get_annotation_resources | 0.020 | 0.003 | 0.635 | |
| get_complex_genes | 0.506 | 0.022 | 2.363 | |
| get_complex_resources | 0.036 | 0.002 | 0.727 | |
| get_db | 0 | 0 | 0 | |
| get_enzsub_resources | 0.021 | 0.002 | 0.608 | |
| get_interaction_resources | 0.023 | 0.003 | 0.535 | |
| get_intercell_categories | 0.087 | 0.013 | 0.320 | |
| get_intercell_generic_categories | 0.011 | 0.001 | 0.012 | |
| get_intercell_resources | 0.042 | 0.002 | 0.555 | |
| get_ontology_db | 0.003 | 0.000 | 0.004 | |
| get_resources | 0.021 | 0.002 | 0.569 | |
| get_signed_ptms | 1.702 | 0.025 | 2.238 | |
| giant_component | 3.613 | 0.126 | 6.445 | |
| go_annot_download | 3.929 | 0.186 | 4.198 | |
| go_annot_slim | 0.000 | 0.001 | 0.001 | |
| go_ontology_download | 0.003 | 0.000 | 0.003 | |
| guide2pharma_download | 0.003 | 0.000 | 0.004 | |
| harmonizome_download | 0.003 | 0.001 | 0.003 | |
| has_extra_attrs | 1.988 | 0.025 | 2.013 | |
| homologene_download | 0.003 | 0.000 | 0.003 | |
| homologene_raw | 0.006 | 0.001 | 0.006 | |
| homologene_uniprot_orthology | 0.003 | 0.000 | 0.004 | |
| hpo_download | 0.871 | 0.085 | 2.297 | |
| htridb_download | 0.003 | 0.000 | 0.003 | |
| import_all_interactions | 0.643 | 0.038 | 5.873 | |
| import_intercell_network | 0.003 | 0.001 | 0.003 | |
| import_kinaseextra_interactions | 0.517 | 0.029 | 3.202 | |
| import_ligrecextra_interactions | 0.208 | 0.022 | 1.974 | |
| import_lncrna_mrna_interactions | 0.134 | 0.018 | 0.906 | |
| import_mirnatarget_interactions | 0.254 | 0.019 | 1.963 | |
| import_omnipath_annotations | 0.141 | 0.012 | 1.030 | |
| import_omnipath_complexes | 0.177 | 0.013 | 1.854 | |
| import_omnipath_enzsub | 0.329 | 0.004 | 0.814 | |
| import_omnipath_interactions | 0.095 | 0.003 | 0.577 | |
| import_omnipath_intercell | 0.142 | 0.014 | 0.709 | |
| import_pathwayextra_interactions | 0.242 | 0.019 | 2.278 | |
| import_post_translational_interactions | 0.248 | 0.020 | 2.480 | |
| import_small_molecule_protein_interactions | 0.133 | 0.010 | 0.377 | |
| import_tf_mirna_interactions | 0.209 | 0.017 | 1.273 | |
| import_tf_target_interactions | 0.394 | 0.028 | 2.693 | |
| import_transcriptional_interactions | 0.830 | 0.037 | 4.495 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.012 | 0.001 | 0.013 | |
| interaction_graph | 0.141 | 0.003 | 0.724 | |
| interaction_types | 0.012 | 0.001 | 0.013 | |
| intercell_categories | 0.017 | 0.001 | 0.017 | |
| intercell_consensus_filter | 0.463 | 0.037 | 2.801 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.011 | 0.001 | 0.012 | |
| is_trembl | 0.010 | 0.001 | 0.010 | |
| is_uniprot | 0.004 | 0.001 | 0.003 | |
| kegg_info | 0.003 | 0.000 | 0.003 | |
| kegg_open | 0.003 | 0.000 | 0.003 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.003 | 0.000 | 0.003 | |
| kegg_pathway_list | 0.003 | 0.000 | 0.003 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.026 | 0.005 | 4.391 | |
| kegg_process | 0.006 | 0.000 | 0.007 | |
| latin_name | 0.012 | 0.000 | 0.012 | |
| load_db | 0.022 | 0.000 | 0.022 | |
| ncbi_taxid | 0.030 | 0.001 | 0.032 | |
| nichenet_build_model | 0.001 | 0.000 | 0.000 | |
| nichenet_expression_data | 0.004 | 0.001 | 0.005 | |
| nichenet_gr_network | 0.009 | 0.001 | 0.011 | |
| nichenet_gr_network_evex | 0.003 | 0.000 | 0.004 | |
| nichenet_gr_network_harmonizome | 0.004 | 0.001 | 0.003 | |
| nichenet_gr_network_htridb | 0.003 | 0.000 | 0.003 | |
| nichenet_gr_network_omnipath | 4.202 | 0.298 | 6.534 | |
| nichenet_gr_network_pathwaycommons | 0.004 | 0.001 | 0.005 | |
| nichenet_gr_network_regnetwork | 0.004 | 0.001 | 0.005 | |
| nichenet_gr_network_remap | 0.004 | 0.000 | 0.005 | |
| nichenet_gr_network_trrust | 0.003 | 0.001 | 0.004 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.010 | 0.001 | 0.011 | |
| nichenet_lr_network_guide2pharma | 0.003 | 0.000 | 0.003 | |
| nichenet_lr_network_omnipath | 0.009 | 0.002 | 0.010 | |
| nichenet_lr_network_ramilowski | 0.003 | 0.000 | 0.004 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.014 | 0.002 | 0.016 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.009 | 0.001 | 0.009 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.010 | 0.001 | 0.010 | |
| nichenet_signaling_network_cpdb | 0.003 | 0.001 | 0.003 | |
| nichenet_signaling_network_evex | 0.003 | 0.000 | 0.003 | |
| nichenet_signaling_network_harmonizome | 0.003 | 0.001 | 0.003 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 3.161 | 0.228 | 8.500 | |
| nichenet_signaling_network_pathwaycommons | 0.004 | 0.001 | 0.004 | |
| nichenet_signaling_network_vinayagam | 0.003 | 0.000 | 0.003 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.046 | 0.003 | 0.093 | |
| oma_code | 0.005 | 0.000 | 0.006 | |
| oma_organisms | 0.018 | 0.001 | 0.018 | |
| oma_pairwise | 0.003 | 0.000 | 0.003 | |
| oma_pairwise_genesymbols | 0.003 | 0.001 | 0.003 | |
| oma_pairwise_translated | 0.003 | 0.000 | 0.003 | |
| omnipath | 1.518 | 0.009 | 1.527 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.002 | 0.000 | 0.002 | |
| omnipath_cache_clean_db | 0.049 | 0.002 | 0.050 | |
| omnipath_cache_download_ready | 0.177 | 0.013 | 0.224 | |
| omnipath_cache_filter_versions | 0.031 | 0.004 | 0.085 | |
| omnipath_cache_get | 0.051 | 0.004 | 0.055 | |
| omnipath_cache_key | 0 | 0 | 0 | |
| omnipath_cache_latest_or_new | 0.020 | 0.002 | 0.023 | |
| omnipath_cache_load | 0.232 | 0.016 | 2.838 | |
| omnipath_cache_move_in | 0.056 | 0.010 | 0.073 | |
| omnipath_cache_remove | 0.056 | 0.005 | 0.066 | |
| omnipath_cache_save | 0.051 | 0.007 | 0.077 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.047 | 0.004 | 0.057 | |
| omnipath_cache_update_status | 0.029 | 0.004 | 0.032 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_get_config_path | 0 | 0 | 0 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.001 | 0.000 | |
| omnipath_msg | 0.002 | 0.000 | 0.002 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.007 | 0.001 | 0.009 | |
| omnipath_set_console_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_set_logfile_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.030 | 0.001 | 0.030 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0.001 | 0.000 | 0.000 | |