| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:38 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 1422/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.13.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 3.13.0 |
| 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_3.13.0.tar.gz |
| StartedAt: 2024-05-02 08:35:05 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 09:06:02 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 1857.2 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_3.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.0’
* 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
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-02 08:36:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:03] [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
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 08:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:33] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 08:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-02 08:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-02 08:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-02 08:36:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-02 08:36:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 08:36:34] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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, 1 WARNING, 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-x86_64/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-05-01 16:03:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-01 16:03:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:08] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-01 16:03:08] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:08] [TRACE] [OmnipathR] Contains 1 files. [2024-05-01 16:03:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-01 16:03:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-01 16:03:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-01 16:03:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-01 16:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-01 16:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-01 16:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-01 16:03:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:10] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Contains 1 files. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-01 16:03:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-01 16:03:14] [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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2024-05-02 09:03:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 09:03:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 09:03:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-02 09:03:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 09:03:50] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-02 09:03:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-02 09:03:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-02 09:03:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-02 09:03:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-02 09:03:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-02 09:03:51] [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
21.619 1.639 102.199
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.002 | 0.001 | |
| all_uniprot_acs | 0.052 | 0.005 | 0.061 | |
| all_uniprots | 0.027 | 0.002 | 0.037 | |
| ancestors | 0.026 | 0.002 | 0.031 | |
| annotated_network | 3.117 | 0.288 | 106.059 | |
| annotation_categories | 101.301 | 0.678 | 119.805 | |
| biomart_query | 1.345 | 0.126 | 3.092 | |
| bioplex1 | 0.026 | 0.002 | 0.034 | |
| bioplex2 | 0.029 | 0.003 | 0.039 | |
| bioplex3 | 0.027 | 0.003 | 0.039 | |
| bioplex_all | 0.028 | 0.002 | 0.037 | |
| bioplex_hct116_1 | 0.025 | 0.003 | 0.033 | |
| bma_motif_es | 0.630 | 0.052 | 1.534 | |
| bma_motif_vs | 0.332 | 0.010 | 0.883 | |
| collectri | 311.021 | 3.424 | 370.266 | |
| common_name | 0.043 | 0.001 | 0.052 | |
| consensuspathdb_download | 0.000 | 0.002 | 0.001 | |
| consensuspathdb_raw_table | 0.025 | 0.002 | 0.032 | |
| curated_ligand_receptor_interactions | 9.256 | 0.446 | 18.790 | |
| curated_ligrec_stats | 58.623 | 2.022 | 128.647 | |
| database_summary | 2.760 | 0.072 | 4.327 | |
| descendants | 0.075 | 0.003 | 0.091 | |
| dorothea | 163.987 | 1.725 | 272.518 | |
| ensembl_dataset | 0.016 | 0.001 | 0.019 | |
| ensembl_id_mapping_table | 1.464 | 0.104 | 13.066 | |
| ensembl_id_type | 0.004 | 0.000 | 0.007 | |
| ensembl_name | 0.090 | 0.002 | 0.114 | |
| ensembl_organisms | 0.276 | 0.005 | 0.386 | |
| ensembl_organisms_raw | 0.271 | 0.008 | 0.416 | |
| ensembl_orthology | 0.001 | 0.001 | 0.001 | |
| enzsub_graph | 4.144 | 0.147 | 16.979 | |
| evex_download | 0.028 | 0.003 | 0.069 | |
| evidences | 0.000 | 0.001 | 0.001 | |
| extra_attr_values | 29.002 | 0.507 | 52.486 | |
| extra_attrs | 15.824 | 0.196 | 31.084 | |
| extra_attrs_to_cols | 25.869 | 0.206 | 41.509 | |
| filter_by_resource | 14.077 | 0.292 | 16.942 | |
| filter_extra_attrs | 54.690 | 0.383 | 66.542 | |
| filter_intercell | 8.757 | 0.733 | 11.313 | |
| filter_intercell_network | 0.056 | 0.005 | 0.074 | |
| find_all_paths | 12.693 | 0.306 | 14.772 | |
| from_evidences | 0.001 | 0.001 | 0.002 | |
| get_annotation_resources | 0.132 | 0.010 | 0.755 | |
| get_complex_genes | 2.103 | 0.131 | 3.320 | |
| get_complex_resources | 0.135 | 0.007 | 0.764 | |
| get_db | 0.001 | 0.001 | 0.001 | |
| get_enzsub_resources | 0.180 | 0.009 | 0.850 | |
| get_interaction_resources | 0.134 | 0.011 | 0.813 | |
| get_intercell_categories | 0.662 | 0.079 | 1.195 | |
| get_intercell_generic_categories | 0.076 | 0.005 | 0.092 | |
| get_intercell_resources | 0.135 | 0.006 | 0.658 | |
| get_ontology_db | 0.028 | 0.002 | 0.033 | |
| get_resources | 0.186 | 0.010 | 0.812 | |
| get_signed_ptms | 12.036 | 0.137 | 14.825 | |
| giant_component | 22.360 | 0.520 | 27.023 | |
| go_annot_download | 13.974 | 1.128 | 21.987 | |
| go_annot_slim | 0.000 | 0.001 | 0.002 | |
| go_ontology_download | 0.025 | 0.003 | 0.028 | |
| guide2pharma_download | 0.025 | 0.003 | 0.030 | |
| harmonizome_download | 0.025 | 0.002 | 0.030 | |
| has_extra_attrs | 16.044 | 0.207 | 18.893 | |
| homologene_download | 0.025 | 0.003 | 0.043 | |
| homologene_raw | 0.040 | 0.004 | 0.058 | |
| homologene_uniprot_orthology | 0.026 | 0.003 | 0.048 | |
| hpo_download | 3.524 | 0.390 | 4.553 | |
| htridb_download | 0.024 | 0.002 | 0.029 | |
| import_all_interactions | 4.260 | 0.225 | 6.705 | |
| import_intercell_network | 0.026 | 0.003 | 0.030 | |
| import_kinaseextra_interactions | 2.730 | 0.131 | 4.608 | |
| import_ligrecextra_interactions | 1.291 | 0.081 | 2.611 | |
| import_lncrna_mrna_interactions | 0.921 | 0.064 | 1.927 | |
| import_mirnatarget_interactions | 1.918 | 0.087 | 3.405 | |
| import_omnipath_annotations | 0.886 | 0.051 | 1.913 | |
| import_omnipath_complexes | 1.050 | 0.066 | 2.545 | |
| import_omnipath_enzsub | 2.505 | 0.026 | 3.616 | |
| import_omnipath_interactions | 0.554 | 0.013 | 1.217 | |
| import_omnipath_intercell | 0.889 | 0.062 | 1.582 | |
| import_pathwayextra_interactions | 1.489 | 0.089 | 3.132 | |
| import_post_translational_interactions | 1.551 | 0.091 | 3.075 | |
| import_small_molecule_protein_interactions | 0.908 | 0.047 | 1.387 | |
| import_tf_mirna_interactions | 1.396 | 0.074 | 2.731 | |
| import_tf_target_interactions | 2.770 | 0.107 | 4.489 | |
| import_transcriptional_interactions | 5.184 | 0.166 | 7.466 | |
| inbiomap_download | 0.001 | 0.001 | 0.001 | |
| inbiomap_raw | 0.000 | 0.000 | 0.001 | |
| interaction_datasets | 0.144 | 0.005 | 0.169 | |
| interaction_graph | 0.736 | 0.011 | 1.489 | |
| interaction_types | 0.076 | 0.005 | 0.112 | |
| intercell_categories | 0.108 | 0.004 | 0.160 | |
| intercell_consensus_filter | 2.232 | 0.180 | 3.411 | |
| is_ontology_id | 0.000 | 0.001 | 0.001 | |
| is_swissprot | 0.135 | 0.012 | 0.224 | |
| is_trembl | 0.067 | 0.004 | 0.086 | |
| is_uniprot | 0.030 | 0.003 | 0.039 | |
| kegg_info | 0.028 | 0.002 | 0.033 | |
| kegg_open | 0.026 | 0.002 | 0.035 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.028 | 0.003 | 0.036 | |
| kegg_pathway_list | 0.029 | 0.003 | 0.037 | |
| kegg_pathways_download | 0.001 | 0.000 | 0.001 | |
| kegg_picture | 0.149 | 0.016 | 2.127 | |
| kegg_process | 0.048 | 0.004 | 0.052 | |
| latin_name | 0.079 | 0.001 | 0.080 | |
| load_db | 0.167 | 0.006 | 0.292 | |
| ncbi_taxid | 0.082 | 0.001 | 0.083 | |
| nichenet_build_model | 0.001 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.024 | 0.002 | 0.028 | |
| nichenet_gr_network | 0.076 | 0.006 | 0.093 | |
| nichenet_gr_network_evex | 0.090 | 0.003 | 0.127 | |
| nichenet_gr_network_harmonizome | 0.029 | 0.003 | 0.034 | |
| nichenet_gr_network_htridb | 0.026 | 0.002 | 0.031 | |
| nichenet_gr_network_omnipath | 25.664 | 0.773 | 30.899 | |
| nichenet_gr_network_pathwaycommons | 0.025 | 0.002 | 0.031 | |
| nichenet_gr_network_regnetwork | 0.026 | 0.003 | 0.036 | |
| nichenet_gr_network_remap | 0.027 | 0.002 | 0.034 | |
| nichenet_gr_network_trrust | 0.026 | 0.002 | 0.032 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0.001 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.134 | 0.010 | 0.170 | |
| nichenet_lr_network_guide2pharma | 0.026 | 0.002 | 0.031 | |
| nichenet_lr_network_omnipath | 0.077 | 0.006 | 0.090 | |
| nichenet_lr_network_ramilowski | 0.027 | 0.002 | 0.032 | |
| nichenet_main | 0.000 | 0.001 | 0.002 | |
| nichenet_networks | 0.126 | 0.012 | 0.163 | |
| nichenet_optimization | 0.001 | 0.001 | 0.000 | |
| nichenet_remove_orphan_ligands | 0.079 | 0.006 | 0.094 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.082 | 0.006 | 0.104 | |
| nichenet_signaling_network_cpdb | 0.027 | 0.002 | 0.034 | |
| nichenet_signaling_network_evex | 0.027 | 0.003 | 0.035 | |
| nichenet_signaling_network_harmonizome | 0.029 | 0.002 | 0.033 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.002 | |
| nichenet_signaling_network_omnipath | 19.546 | 0.524 | 24.163 | |
| nichenet_signaling_network_pathwaycommons | 0.027 | 0.003 | 0.033 | |
| nichenet_signaling_network_vinayagam | 0.027 | 0.002 | 0.036 | |
| nichenet_test | 0.000 | 0.001 | 0.001 | |
| nichenet_workarounds | 0.000 | 0.001 | 0.001 | |
| obo_parser | 0.196 | 0.010 | 0.305 | |
| oma_code | 0.111 | 0.003 | 0.135 | |
| oma_organisms | 0.120 | 0.004 | 0.152 | |
| oma_pairwise | 0.027 | 0.003 | 0.036 | |
| oma_pairwise_genesymbols | 0.025 | 0.002 | 0.028 | |
| omnipath | 9.881 | 0.067 | 11.468 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.016 | 0.001 | 0.022 | |
| omnipath_cache_clean_db | 0.286 | 0.015 | 0.592 | |
| omnipath_cache_download_ready | 1.176 | 0.094 | 1.574 | |
| omnipath_cache_filter_versions | 0.248 | 0.027 | 0.337 | |
| omnipath_cache_get | 0.211 | 0.023 | 0.275 | |
| omnipath_cache_key | 0.003 | 0.001 | 0.004 | |
| omnipath_cache_latest_or_new | 0.166 | 0.017 | 0.230 | |
| omnipath_cache_load | 1.005 | 0.049 | 2.151 | |
| omnipath_cache_move_in | 0.449 | 0.043 | 0.621 | |
| omnipath_cache_remove | 0.248 | 0.027 | 0.396 | |
| omnipath_cache_save | 0.427 | 0.036 | 0.746 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.189 | 0.019 | 0.224 | |
| omnipath_cache_update_status | 0.285 | 0.022 | 0.339 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.001 | |
| omnipath_get_config_path | 0.000 | 0.001 | 0.004 | |
| omnipath_load_config | 0.001 | 0.001 | 0.000 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.002 | 0.000 | 0.002 | |
| omnipath_msg | 0.014 | 0.001 | 0.017 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0.000 | 0.001 | 0.002 | |
| omnipath_set_cachedir | 0.071 | 0.007 | 0.091 | |
| omnipath_set_console_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.004 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_show_db | 0.127 | 0.002 | 0.141 | |
| omnipath_unlock_cache_db | 0.001 | 0.001 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.002 | |
| ontology_name_id | 0.002 | 0.001 | 0.003 | |