Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-08-08 11:41 -0400 (Thu, 08 Aug 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" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4402 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1436/2254 | 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: OmnipathR |
Version: 3.13.1 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz |
StartedAt: 2024-08-08 03:57:08 -0400 (Thu, 08 Aug 2024) |
EndedAt: 2024-08-08 04:10:39 -0400 (Thu, 08 Aug 2024) |
EllapsedTime: 811.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 [2024-08-08 03:57:37] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 03:57:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:37] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Contains 1 files. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 03:57:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:37] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-08-08 03:57:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-08 03:57:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-08 03:57:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-08 03:57:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-08 03:57:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:38] [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 [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Contains 1 files. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-08 03:57:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 03:57:54] [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 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log' for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Contains 1 files. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-07 15:45:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:16] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Contains 1 files. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-07 15:45:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-07 15:45:18] [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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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) [2024-08-08 04:09:39] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 04:09:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:39] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Contains 1 files. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-08-08 04:09:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:39] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-08-08 04:09:39] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-08-08 04:09:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:39] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-08-08 04:09:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-08-08 04:09:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-08-08 04:09:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-08-08 04:09:40] [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 12.42 1.54 31.51
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0.01 | 0.00 | 0.01 | |
all_uniprot_acs | 0.03 | 0.02 | 0.05 | |
all_uniprots | 0.01 | 0.00 | 0.02 | |
ancestors | 0.02 | 0.00 | 0.01 | |
annotated_network | 1.95 | 0.17 | 5.55 | |
annotation_categories | 76.34 | 0.01 | 77.01 | |
biomart_query | 0.82 | 0.07 | 13.86 | |
bioplex1 | 0.01 | 0.00 | 0.02 | |
bioplex2 | 0.00 | 0.00 | 0.01 | |
bioplex3 | 0.03 | 0.00 | 0.03 | |
bioplex_all | 0.02 | 0.00 | 0.02 | |
bioplex_hct116_1 | 0.00 | 0.01 | 0.01 | |
bma_motif_es | 0.43 | 0.11 | 1.17 | |
bma_motif_vs | 0.15 | 0.00 | 0.77 | |
collectri | 140.66 | 2.08 | 143.31 | |
common_name | 0.01 | 0.00 | 0.02 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.02 | 0.00 | 0.02 | |
curated_ligand_receptor_interactions | 4.43 | 0.44 | 10.86 | |
curated_ligrec_stats | 29.96 | 2.34 | 76.82 | |
database_summary | 1.45 | 0.13 | 2.33 | |
descendants | 0.01 | 0.00 | 0.01 | |
dorothea | 78.61 | 1.16 | 81.00 | |
ensembl_dataset | 0.03 | 0.00 | 0.04 | |
ensembl_id_mapping_table | 0.92 | 0.17 | 11.05 | |
ensembl_id_type | 0 | 0 | 0 | |
ensembl_name | 0.05 | 0.00 | 0.05 | |
ensembl_organisms | 0.20 | 0.01 | 0.32 | |
ensembl_organisms_raw | 0.16 | 0.00 | 0.19 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.23 | 0.15 | 4.56 | |
evex_download | 0.03 | 0.00 | 0.03 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 13.49 | 0.35 | 14.40 | |
extra_attrs | 8.56 | 0.05 | 8.71 | |
extra_attrs_to_cols | 14.05 | 0.06 | 14.64 | |
filter_by_resource | 8.87 | 0.35 | 15.22 | |
filter_extra_attrs | 28.11 | 0.31 | 31.22 | |
filter_intercell | 7.82 | 0.56 | 17.30 | |
filter_intercell_network | 0.03 | 0.02 | 0.08 | |
find_all_paths | 6.62 | 0.14 | 7.14 | |
from_evidences | 0 | 0 | 0 | |
get_annotation_resources | 0.08 | 0.00 | 0.50 | |
get_complex_genes | 1.50 | 0.08 | 2.33 | |
get_complex_resources | 0.06 | 0.00 | 0.50 | |
get_db | 0 | 0 | 0 | |
get_enzsub_resources | 0.06 | 0.00 | 0.46 | |
get_interaction_resources | 0.08 | 0.00 | 0.49 | |
get_intercell_categories | 0.72 | 0.09 | 1.37 | |
get_intercell_generic_categories | 0.10 | 0.00 | 0.18 | |
get_intercell_resources | 0.07 | 0.00 | 0.50 | |
get_ontology_db | 0.02 | 0.00 | 0.03 | |
get_resources | 0.08 | 0.00 | 0.56 | |
get_signed_ptms | 6.17 | 0.09 | 6.90 | |
giant_component | 11.72 | 0.33 | 13.38 | |
go_annot_download | 11.14 | 0.92 | 10.68 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.01 | 0.00 | 0.02 | |
guide2pharma_download | 0.00 | 0.00 | 0.03 | |
harmonizome_download | 0.00 | 0.00 | 0.02 | |
has_extra_attrs | 6.82 | 0.02 | 6.98 | |
homologene_download | 0.02 | 0.00 | 0.01 | |
homologene_raw | 0.03 | 0.00 | 0.03 | |
homologene_uniprot_orthology | 0.01 | 0.02 | 0.03 | |
hpo_download | 2.32 | 0.15 | 2.75 | |
htridb_download | 0.03 | 0.00 | 0.04 | |
import_all_interactions | 2.55 | 0.13 | 4.03 | |
import_intercell_network | 0.00 | 0.01 | 0.01 | |
import_kinaseextra_interactions | 1.51 | 0.14 | 2.67 | |
import_ligrecextra_interactions | 0.84 | 0.02 | 1.79 | |
import_lncrna_mrna_interactions | 0.65 | 0.12 | 1.35 | |
import_mirnatarget_interactions | 0.98 | 0.10 | 2.00 | |
import_omnipath_annotations | 0.47 | 0.08 | 1.27 | |
import_omnipath_complexes | 0.61 | 0.01 | 1.59 | |
import_omnipath_enzsub | 1.11 | 0.00 | 1.52 | |
import_omnipath_interactions | 0.23 | 0.02 | 0.80 | |
import_omnipath_intercell | 0.60 | 0.11 | 1.12 | |
import_pathwayextra_interactions | 0.85 | 0.14 | 2.13 | |
import_post_translational_interactions | 0.80 | 0.12 | 1.90 | |
import_small_molecule_protein_interactions | 0.47 | 0.05 | 0.83 | |
import_tf_mirna_interactions | 0.77 | 0.12 | 1.72 | |
import_tf_target_interactions | 1.18 | 0.11 | 2.20 | |
import_transcriptional_interactions | 2.52 | 0.19 | 3.57 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.06 | 0.00 | 0.06 | |
interaction_graph | 0.33 | 0.03 | 0.76 | |
interaction_types | 0.05 | 0.02 | 0.07 | |
intercell_categories | 0.03 | 0.04 | 0.07 | |
intercell_consensus_filter | 1.44 | 0.13 | 2.13 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.03 | 0.03 | 0.07 | |
is_trembl | 0.03 | 0.02 | 0.04 | |
is_uniprot | 0.02 | 0.01 | 0.04 | |
kegg_info | 0.00 | 0.00 | 0.03 | |
kegg_open | 0 | 0 | 0 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.02 | 0.00 | 0.01 | |
kegg_pathway_list | 0.02 | 0.02 | 0.03 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.09 | 0.01 | 2.03 | |
kegg_process | 0.03 | 0.00 | 0.04 | |
latin_name | 0.06 | 0.00 | 0.06 | |
load_db | 0.11 | 0.03 | 0.14 | |
ncbi_taxid | 0.06 | 0.00 | 0.07 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.02 | 0.00 | 0.01 | |
nichenet_gr_network | 0.04 | 0.02 | 0.07 | |
nichenet_gr_network_evex | 0.02 | 0.00 | 0.01 | |
nichenet_gr_network_harmonizome | 0.01 | 0.02 | 0.03 | |
nichenet_gr_network_htridb | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_omnipath | 14.08 | 0.73 | 15.20 | |
nichenet_gr_network_pathwaycommons | 0.03 | 0.00 | 0.03 | |
nichenet_gr_network_regnetwork | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_remap | 0.03 | 0.00 | 0.03 | |
nichenet_gr_network_trrust | 0.00 | 0.00 | 0.01 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.06 | 0.00 | 0.07 | |
nichenet_lr_network_guide2pharma | 0.03 | 0.00 | 0.03 | |
nichenet_lr_network_omnipath | 0.06 | 0.00 | 0.06 | |
nichenet_lr_network_ramilowski | 0.02 | 0.02 | 0.03 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.09 | 0.00 | 0.11 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.08 | 0.00 | 0.08 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.05 | 0.00 | 0.06 | |
nichenet_signaling_network_cpdb | 0.02 | 0.00 | 0.01 | |
nichenet_signaling_network_evex | 0.01 | 0.00 | 0.02 | |
nichenet_signaling_network_harmonizome | 0.00 | 0.01 | 0.01 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 9.02 | 0.78 | 10.44 | |
nichenet_signaling_network_pathwaycommons | 0.02 | 0.00 | 0.02 | |
nichenet_signaling_network_vinayagam | 0.01 | 0.00 | 0.03 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.09 | 0.02 | 0.25 | |
oma_code | 0.04 | 0.00 | 0.03 | |
oma_organisms | 0.07 | 0.00 | 0.09 | |
oma_pairwise | 0.04 | 0.00 | 0.04 | |
oma_pairwise_genesymbols | 0.02 | 0.00 | 0.02 | |
oma_pairwise_translated | 0.03 | 0.00 | 0.03 | |
omnipath | 3.36 | 0.03 | 3.42 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0 | 0 | 0 | |
omnipath_cache_clean_db | 0.08 | 0.00 | 0.09 | |
omnipath_cache_download_ready | 0.60 | 0.11 | 0.96 | |
omnipath_cache_filter_versions | 0.19 | 0.03 | 0.26 | |
omnipath_cache_get | 0.22 | 0.00 | 0.27 | |
omnipath_cache_key | 0 | 0 | 0 | |
omnipath_cache_latest_or_new | 0.11 | 0.02 | 0.14 | |
omnipath_cache_load | 0.55 | 0.07 | 1.42 | |
omnipath_cache_move_in | 0.23 | 0.04 | 0.39 | |
omnipath_cache_remove | 0.22 | 0.03 | 0.33 | |
omnipath_cache_save | 0.23 | 0.04 | 0.37 | |
omnipath_cache_search | 0 | 0 | 0 | |
omnipath_cache_set_ext | 0.11 | 0.05 | 0.24 | |
omnipath_cache_update_status | 0.14 | 0.03 | 0.20 | |
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 | 0 | 0 | |
omnipath_msg | 0.02 | 0.00 | 0.02 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.03 | 0.02 | 0.06 | |
omnipath_set_console_loglevel | 0 | 0 | 0 | |
omnipath_set_logfile_loglevel | 0 | 0 | 0 | |
omnipath_set_loglevel | 0.02 | 0.00 | 0.01 | |
omnipath_show_db | 0.04 | 0.00 | 0.05 | |
omnipath_unlock_cache_db | 0 | 0 | 0 | |
only_from | 0 | 0 | 0 | |
ontology_ensure_id | 0 | 0 | 0 | |
ontology_ensure_name | 0 | 0 | 0 | |
ontology_name_id | 0 | 0 | 0 | |