Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:05 -0500 (Thu, 06 Feb 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
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
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | 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: 3.14.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz |
StartedAt: 2025-02-04 00:50:58 -0500 (Tue, 04 Feb 2025) |
EndedAt: 2025-02-04 01:16:37 -0500 (Tue, 04 Feb 2025) |
EllapsedTime: 1539.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OmnipathR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.14.0’ * 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 ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Contains 1 files. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-04 00:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:20] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Contains 1 files. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-04 00:51:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 00:51:32] [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 86.115 0.067 88.151 omnipath-interactions 40.088 1.708 94.112 curated_ligrec_stats 30.028 1.097 110.612 go_annot_download 18.995 0.758 29.783 nichenet_signaling_network_omnipath 16.740 0.153 26.568 nichenet_gr_network_omnipath 15.798 0.329 19.303 pivot_annotations 15.067 0.698 46.356 filter_extra_attrs 14.867 0.278 15.915 omnipath_for_cosmos 13.966 0.541 49.655 with_extra_attrs 10.831 0.196 15.258 extra_attr_values 9.437 0.265 14.627 giant_component 8.451 0.195 15.397 translate_ids_multi 8.128 0.161 25.886 has_extra_attrs 8.122 0.067 8.189 extra_attrs_to_cols 8.020 0.107 8.129 print_interactions 7.838 0.159 16.806 omnipath_query 5.884 0.081 5.988 static_table 5.574 0.335 11.859 extra_attrs 5.547 0.101 5.649 filter_by_resource 5.203 0.269 7.811 filter_intercell 5.043 0.289 9.210 curated_ligand_receptor_interactions 4.286 0.307 18.010 uniprot_full_id_mapping_table 1.400 0.049 23.648 ensembl_id_mapping_table 1.166 0.035 27.117 translate_ids 1.072 0.014 19.125 all_uniprots 0.921 0.087 20.166 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Contains 8 files. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 15:43:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:43] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 15:43:46] [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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2024 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://r.omnipathdb.org/ > # Git repo: https://github.com/saezlab/OmnipathR > # > > > library(testthat) > library(OmnipathR) [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Contains 21 files. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-04 01:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 01:05:53] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 15.599 0.947 51.803
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.013 | 0.002 | 0.015 | |
all_uniprots | 0.921 | 0.087 | 20.166 | |
ancestors | 0.008 | 0.003 | 0.011 | |
annotated_network | 0.850 | 0.099 | 4.422 | |
annotation_categories | 86.115 | 0.067 | 88.151 | |
annotation_resources | 0.086 | 0.007 | 0.820 | |
annotations | 0.335 | 0.041 | 1.490 | |
biomart_query | 0.771 | 0.070 | 3.793 | |
bioplex1 | 0.007 | 0.001 | 0.007 | |
bioplex2 | 0.007 | 0.000 | 0.007 | |
bioplex3 | 0.033 | 0.000 | 0.033 | |
bioplex_all | 0.007 | 0.000 | 0.007 | |
bioplex_hct116_1 | 0.006 | 0.000 | 0.007 | |
bma_motif_es | 0.399 | 0.055 | 1.551 | |
bma_motif_vs | 0.193 | 0.001 | 0.943 | |
chalmers_gem | 0.008 | 0.000 | 0.008 | |
chalmers_gem_id_mapping_table | 0.007 | 0.000 | 0.007 | |
chalmers_gem_id_type | 0.001 | 0.000 | 0.001 | |
chalmers_gem_metabolites | 0.006 | 0.000 | 0.006 | |
chalmers_gem_network | 0.007 | 0.000 | 0.007 | |
chalmers_gem_raw | 0.007 | 0.000 | 0.007 | |
chalmers_gem_reactions | 0.007 | 0.000 | 0.007 | |
common_name | 0.049 | 0.000 | 0.049 | |
complex_genes | 0.447 | 0.011 | 2.396 | |
complex_resources | 0.128 | 0.003 | 0.819 | |
complexes | 0.146 | 0.003 | 0.836 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.007 | 0.000 | 0.007 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 4.286 | 0.307 | 18.010 | |
curated_ligrec_stats | 30.028 | 1.097 | 110.612 | |
database_summary | 1.342 | 0.019 | 4.192 | |
descendants | 0.008 | 0.000 | 0.008 | |
ensembl_dataset | 0.01 | 0.00 | 0.01 | |
ensembl_id_mapping_table | 1.166 | 0.035 | 27.117 | |
ensembl_id_type | 0.003 | 0.000 | 0.002 | |
ensembl_name | 0.055 | 0.000 | 0.055 | |
ensembl_organisms | 0.101 | 0.000 | 0.101 | |
ensembl_organisms_raw | 0.120 | 0.002 | 0.122 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 1.741 | 0.092 | 4.603 | |
enzsub_resources | 0.117 | 0.002 | 0.884 | |
enzyme_substrate | 0.934 | 0.033 | 1.620 | |
evex_download | 0.007 | 0.000 | 0.007 | |
evidences | 0.000 | 0.000 | 0.001 | |
extra_attr_values | 9.437 | 0.265 | 14.627 | |
extra_attrs | 5.547 | 0.101 | 5.649 | |
extra_attrs_to_cols | 8.020 | 0.107 | 8.129 | |
filter_by_resource | 5.203 | 0.269 | 7.811 | |
filter_extra_attrs | 14.867 | 0.278 | 15.915 | |
filter_intercell | 5.043 | 0.289 | 9.210 | |
filter_intercell_network | 0.015 | 0.000 | 0.016 | |
find_all_paths | 4.770 | 0.116 | 4.886 | |
from_evidences | 0.001 | 0.000 | 0.000 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.009 | 0.000 | 0.008 | |
giant_component | 8.451 | 0.195 | 15.397 | |
go_annot_download | 18.995 | 0.758 | 29.783 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.034 | 0.000 | 0.034 | |
guide2pharma_download | 0.024 | 0.002 | 0.026 | |
harmonizome_download | 0.024 | 0.001 | 0.025 | |
has_extra_attrs | 8.122 | 0.067 | 8.189 | |
hmdb_id_mapping_table | 0.007 | 0.001 | 0.008 | |
hmdb_id_type | 0.002 | 0.000 | 0.002 | |
hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.007 | 0.000 | 0.007 | |
homologene_download | 0.007 | 0.000 | 0.007 | |
homologene_raw | 0.016 | 0.001 | 0.018 | |
homologene_uniprot_orthology | 0.008 | 0.000 | 0.008 | |
hpo_download | 2.596 | 0.158 | 4.281 | |
htridb_download | 0.008 | 0.001 | 0.008 | |
id_translation_resources | 0.001 | 0.000 | 0.000 | |
id_types | 0.037 | 0.000 | 0.037 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.964 | 0.018 | 1.676 | |
interaction_graph | 0.704 | 0.048 | 1.608 | |
interaction_resources | 0.164 | 0.016 | 0.838 | |
interaction_types | 0.073 | 0.006 | 0.079 | |
intercell | 0.737 | 0.060 | 1.565 | |
intercell_categories | 0.740 | 0.021 | 1.600 | |
intercell_consensus_filter | 1.828 | 0.086 | 4.937 | |
intercell_generic_categories | 0.081 | 0.002 | 0.083 | |
intercell_network | 0.017 | 0.001 | 0.018 | |
intercell_resources | 0.196 | 0.000 | 0.874 | |
intercell_summary | 0.101 | 0.003 | 0.206 | |
is_ontology_id | 0.000 | 0.000 | 0.001 | |
is_swissprot | 0.070 | 0.000 | 0.143 | |
is_trembl | 0.059 | 0.000 | 0.116 | |
is_uniprot | 0.021 | 0.001 | 0.046 | |
kegg_info | 0.019 | 0.000 | 0.039 | |
kegg_open | 0.015 | 0.003 | 0.038 | |
kegg_pathway_annotations | 0.001 | 0.000 | 0.000 | |
kegg_pathway_download | 0.020 | 0.000 | 0.036 | |
kegg_pathway_list | 0.019 | 0.000 | 0.039 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.288 | 0.003 | 4.806 | |
kegg_process | 0.038 | 0.002 | 0.056 | |
latin_name | 0.15 | 0.00 | 0.15 | |
load_db | 0.166 | 0.002 | 0.291 | |
ncbi_taxid | 0.140 | 0.000 | 0.141 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.022 | 0.000 | 0.030 | |
nichenet_gr_network | 0.064 | 0.001 | 0.091 | |
nichenet_gr_network_evex | 0.019 | 0.000 | 0.019 | |
nichenet_gr_network_harmonizome | 0.022 | 0.001 | 0.023 | |
nichenet_gr_network_htridb | 0.020 | 0.000 | 0.021 | |
nichenet_gr_network_omnipath | 15.798 | 0.329 | 19.303 | |
nichenet_gr_network_pathwaycommons | 0.009 | 0.000 | 0.010 | |
nichenet_gr_network_regnetwork | 0.008 | 0.000 | 0.008 | |
nichenet_gr_network_remap | 0.008 | 0.000 | 0.008 | |
nichenet_gr_network_trrust | 0.009 | 0.000 | 0.014 | |
nichenet_ligand_activities | 0.001 | 0.000 | 0.000 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.038 | 0.000 | 0.155 | |
nichenet_lr_network_guide2pharma | 0.014 | 0.000 | 0.064 | |
nichenet_lr_network_omnipath | 0.043 | 0.001 | 0.181 | |
nichenet_lr_network_ramilowski | 0.012 | 0.000 | 0.013 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.071 | 0.001 | 0.072 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.063 | 0.003 | 0.102 | |
nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
nichenet_signaling_network | 0.056 | 0.001 | 0.057 | |
nichenet_signaling_network_cpdb | 0.018 | 0.000 | 0.018 | |
nichenet_signaling_network_evex | 0.025 | 0.001 | 0.050 | |
nichenet_signaling_network_harmonizome | 0.023 | 0.001 | 0.032 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 16.740 | 0.153 | 26.568 | |
nichenet_signaling_network_pathwaycommons | 0.028 | 0.002 | 0.062 | |
nichenet_signaling_network_vinayagam | 0.030 | 0.001 | 0.063 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.331 | 0.016 | 0.711 | |
oma_code | 0.110 | 0.003 | 0.114 | |
oma_organisms | 0.159 | 0.005 | 0.165 | |
oma_pairwise | 0.029 | 0.002 | 0.032 | |
oma_pairwise_genesymbols | 0.026 | 0.001 | 0.027 | |
oma_pairwise_translated | 0.025 | 0.000 | 0.026 | |
omnipath-interactions | 40.088 | 1.708 | 94.112 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.013 | 0.000 | 0.014 | |
omnipath_cache_clean_db | 0.189 | 0.007 | 0.197 | |
omnipath_cache_download_ready | 1.039 | 0.049 | 1.171 | |
omnipath_cache_filter_versions | 0.237 | 0.009 | 0.301 | |
omnipath_cache_get | 0.204 | 0.034 | 0.242 | |
omnipath_cache_key | 0.003 | 0.001 | 0.004 | |
omnipath_cache_latest_or_new | 0.245 | 0.032 | 0.278 | |
omnipath_cache_load | 1.041 | 0.057 | 3.846 | |
omnipath_cache_move_in | 0.289 | 0.029 | 0.378 | |
omnipath_cache_remove | 0.205 | 0.017 | 0.237 | |
omnipath_cache_save | 0.335 | 0.023 | 0.500 | |
omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
omnipath_cache_set_ext | 0.157 | 0.007 | 0.313 | |
omnipath_cache_update_status | 0.220 | 0.014 | 0.337 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0.001 | 0.000 | 0.001 | |
omnipath_for_cosmos | 13.966 | 0.541 | 49.655 | |
omnipath_load_config | 0 | 0 | 0 | |
omnipath_log | 0.001 | 0.000 | 0.000 | |
omnipath_logfile | 0.003 | 0.000 | 0.003 | |
omnipath_msg | 0.010 | 0.001 | 0.011 | |
omnipath_query | 5.884 | 0.081 | 5.988 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0.000 | 0.000 | 0.001 | |
omnipath_set_cachedir | 0.037 | 0.001 | 0.038 | |
omnipath_set_console_loglevel | 0.005 | 0.000 | 0.005 | |
omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.005 | |
omnipath_set_loglevel | 0.002 | 0.000 | 0.003 | |
omnipath_show_db | 0.086 | 0.001 | 0.087 | |
omnipath_unlock_cache_db | 0.000 | 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 | 0.001 | |
ontology_name_id | 0.002 | 0.000 | 0.001 | |
organism_for | 0.075 | 0.001 | 0.075 | |
pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
pivot_annotations | 15.067 | 0.698 | 46.356 | |
preppi_download | 0.001 | 0.000 | 0.001 | |
preppi_filter | 0.001 | 0.000 | 0.001 | |
print_bma_motif_es | 0.387 | 0.043 | 1.511 | |
print_bma_motif_vs | 0.219 | 0.003 | 0.935 | |
print_interactions | 7.838 | 0.159 | 16.806 | |
print_path_es | 0.613 | 0.100 | 2.299 | |
print_path_vs | 2.122 | 0.086 | 4.916 | |
pubmed_open | 3.330 | 0.009 | 3.449 | |
query_info | 0.109 | 0.001 | 0.495 | |
ramilowski_download | 0.001 | 0.000 | 0.001 | |
ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
ramp_id_type | 0.002 | 0.000 | 0.002 | |
ramp_sqlite | 0.001 | 0.000 | 0.000 | |
ramp_table | 0.001 | 0.000 | 0.001 | |
ramp_tables | 0.000 | 0.000 | 0.001 | |
regnetwork_directions | 0.000 | 0.001 | 0.001 | |
regnetwork_download | 0 | 0 | 0 | |
relations_list_to_table | 0.090 | 0.001 | 0.117 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.088 | 0.001 | 0.110 | |
remap_dorothea_download | 0 | 0 | 0 | |
remap_filtered | 0 | 0 | 0 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.186 | 0.006 | 0.842 | |
resources | 0.107 | 0.001 | 0.765 | |
resources_colname | 0.613 | 0.024 | 2.837 | |
resources_in | 2.940 | 0.056 | 2.997 | |
show_network | 0 | 0 | 0 | |
signed_ptms | 4.005 | 0.066 | 4.757 | |
simplify_intercell_network | 0.058 | 0.012 | 0.070 | |
static_table | 5.574 | 0.335 | 11.859 | |
static_tables | 0.041 | 0.000 | 0.046 | |
stitch_actions | 0 | 0 | 0 | |
stitch_links | 0 | 0 | 0 | |
stitch_network | 0.000 | 0.001 | 0.000 | |
stitch_remove_prefixes | 0.006 | 0.000 | 0.006 | |
swap_relations | 0.105 | 0.002 | 0.121 | |
swissprots_only | 0.033 | 0.001 | 0.033 | |
tfcensus_download | 0.191 | 0.006 | 0.395 | |
translate_ids | 1.072 | 0.014 | 19.125 | |
translate_ids_multi | 8.128 | 0.161 | 25.886 | |
trembls_only | 0.062 | 0.000 | 0.062 | |
trrust_download | 0.001 | 0.000 | 0.002 | |
uniprot_full_id_mapping_table | 1.400 | 0.049 | 23.648 | |
uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
uniprot_id_mapping_table | 0.002 | 0.000 | 0.002 | |
uniprot_id_type | 0.004 | 0.000 | 0.005 | |
uniprot_idmapping_id_types | 0.322 | 0.010 | 0.868 | |
unique_intercell_network | 0.001 | 0.000 | 0.002 | |
unnest_evidences | 0.000 | 0.000 | 0.001 | |
uploadlists_id_type | 0.004 | 0.000 | 0.007 | |
vinayagam_download | 0.001 | 0.000 | 0.005 | |
walk_ontology_tree | 0.003 | 0.000 | 0.007 | |
with_extra_attrs | 10.831 | 0.196 | 15.258 | |
with_references | 0.424 | 0.037 | 1.876 | |
zenodo_download | 0.001 | 0.000 | 0.001 | |