Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-03-20 12:05 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
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 | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: OmnipathR |
Version: 3.14.0 |
Command: /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: 2025-03-18 01:25:40 -0400 (Tue, 18 Mar 2025) |
EndedAt: 2025-03-18 01:52:09 -0400 (Tue, 18 Mar 2025) |
EllapsedTime: 1589.3 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 4.4.3 (2025-02-28) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 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 [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Contains 1 files. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 01:26:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:04] [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 [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Contains 1 files. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 01:26:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:26:16] [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 95.864 0.068 97.441 omnipath-interactions 42.926 2.016 92.080 filter_extra_attrs 35.346 0.419 55.077 curated_ligrec_stats 29.773 1.423 103.542 nichenet_signaling_network_omnipath 19.130 0.617 32.232 giant_component 17.206 1.411 24.926 nichenet_gr_network_omnipath 17.820 0.768 24.790 pivot_annotations 15.245 1.016 37.938 go_annot_download 13.049 1.625 17.257 omnipath_for_cosmos 12.577 0.561 27.377 has_extra_attrs 10.483 0.579 21.506 find_all_paths 10.436 0.595 18.388 filter_by_resource 9.726 0.246 15.860 extra_attr_values 9.530 0.232 12.293 filter_intercell 7.997 1.089 12.333 extra_attrs_to_cols 8.190 0.048 8.238 with_extra_attrs 7.196 0.249 9.859 print_interactions 7.140 0.299 15.688 translate_ids_multi 6.011 0.177 15.454 omnipath_query 6.000 0.030 6.035 static_table 5.613 0.302 6.636 extra_attrs 5.192 0.091 5.283 curated_ligand_receptor_interactions 4.426 0.419 15.137 hpo_download 3.314 0.224 5.980 intercell_consensus_filter 2.327 0.136 5.351 ensembl_id_mapping_table 1.180 0.065 10.320 all_uniprots 0.948 0.130 87.653 translate_ids 0.815 0.016 18.367 uniprot_full_id_mapping_table 0.678 0.053 21.588 kegg_picture 0.206 0.006 5.298 * 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 [2025-03-17 16:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 16:30:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:26] [TRACE] [OmnipathR] Contains 8 files. [2025-03-17 16:30:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 16:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 16:30:27] [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). [2025-03-17 16:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:27] [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). [2025-03-17 16:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 16:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:27] [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). [2025-03-17 16:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:27] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-17 16:30:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:30:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 16:30:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:28] [TRACE] [OmnipathR] Contains 1 files. [2025-03-17 16:30:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 16:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-17 16:30:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 16:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-17 16:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-17 16:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 16:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-17 16:30:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:30:29] [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 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 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) [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Contains 21 files. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-18 01:41:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-18 01:41:54] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 11.526 1.124 41.629
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.013 | 0.002 | 0.016 | |
all_uniprots | 0.948 | 0.130 | 87.653 | |
ancestors | 0.009 | 0.002 | 0.011 | |
annotated_network | 0.713 | 0.148 | 3.946 | |
annotation_categories | 95.864 | 0.068 | 97.441 | |
annotation_resources | 0.122 | 0.010 | 0.912 | |
annotations | 0.341 | 0.019 | 1.382 | |
biomart_query | 0.772 | 0.053 | 2.430 | |
bioplex1 | 0.007 | 0.001 | 0.009 | |
bioplex2 | 0.007 | 0.001 | 0.008 | |
bioplex3 | 0.007 | 0.000 | 0.008 | |
bioplex_all | 0.006 | 0.001 | 0.008 | |
bioplex_hct116_1 | 0.040 | 0.009 | 0.050 | |
bma_motif_es | 0.360 | 0.061 | 1.302 | |
bma_motif_vs | 0.243 | 0.003 | 0.950 | |
chalmers_gem | 0.008 | 0.001 | 0.008 | |
chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.007 | |
chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
chalmers_gem_metabolites | 0.007 | 0.000 | 0.007 | |
chalmers_gem_network | 0.008 | 0.000 | 0.007 | |
chalmers_gem_raw | 0.007 | 0.000 | 0.006 | |
chalmers_gem_reactions | 0.007 | 0.000 | 0.007 | |
common_name | 0.028 | 0.000 | 0.028 | |
complex_genes | 0.497 | 0.014 | 2.351 | |
complex_resources | 0.140 | 0.000 | 0.941 | |
complexes | 0.234 | 0.049 | 0.916 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.008 | 0.000 | 0.007 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 4.426 | 0.419 | 15.137 | |
curated_ligrec_stats | 29.773 | 1.423 | 103.542 | |
database_summary | 1.386 | 0.019 | 3.962 | |
descendants | 0.008 | 0.000 | 0.008 | |
ensembl_dataset | 0.011 | 0.000 | 0.011 | |
ensembl_id_mapping_table | 1.180 | 0.065 | 10.320 | |
ensembl_id_type | 0.001 | 0.000 | 0.002 | |
ensembl_name | 0.06 | 0.00 | 0.06 | |
ensembl_organisms | 0.110 | 0.025 | 0.134 | |
ensembl_organisms_raw | 0.124 | 0.011 | 0.135 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 1.913 | 0.046 | 4.174 | |
enzsub_resources | 0.099 | 0.002 | 0.780 | |
enzyme_substrate | 1.186 | 0.010 | 1.882 | |
evex_download | 0.007 | 0.000 | 0.007 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 9.530 | 0.232 | 12.293 | |
extra_attrs | 5.192 | 0.091 | 5.283 | |
extra_attrs_to_cols | 8.190 | 0.048 | 8.238 | |
filter_by_resource | 9.726 | 0.246 | 15.860 | |
filter_extra_attrs | 35.346 | 0.419 | 55.077 | |
filter_intercell | 7.997 | 1.089 | 12.333 | |
filter_intercell_network | 0.015 | 0.001 | 0.016 | |
find_all_paths | 10.436 | 0.595 | 18.388 | |
from_evidences | 0.001 | 0.000 | 0.000 | |
get_db | 0.001 | 0.000 | 0.000 | |
get_ontology_db | 0.019 | 0.000 | 0.019 | |
giant_component | 17.206 | 1.411 | 24.926 | |
go_annot_download | 13.049 | 1.625 | 17.257 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.009 | 0.000 | 0.010 | |
guide2pharma_download | 0.008 | 0.000 | 0.009 | |
harmonizome_download | 0.006 | 0.001 | 0.008 | |
has_extra_attrs | 10.483 | 0.579 | 21.506 | |
hmdb_id_mapping_table | 0.020 | 0.001 | 0.046 | |
hmdb_id_type | 0.005 | 0.000 | 0.009 | |
hmdb_metabolite_fields | 0.000 | 0.000 | 0.001 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.019 | 0.000 | 0.038 | |
homologene_download | 0.021 | 0.000 | 0.038 | |
homologene_raw | 0.044 | 0.001 | 0.091 | |
homologene_uniprot_orthology | 0.019 | 0.002 | 0.044 | |
hpo_download | 3.314 | 0.224 | 5.980 | |
htridb_download | 0.026 | 0.000 | 0.037 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.137 | 0.002 | 0.207 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.923 | 0.028 | 2.129 | |
interaction_graph | 0.758 | 0.047 | 1.726 | |
interaction_resources | 0.320 | 0.017 | 1.421 | |
interaction_types | 0.095 | 0.005 | 0.236 | |
intercell | 0.999 | 0.051 | 2.118 | |
intercell_categories | 0.852 | 0.021 | 1.724 | |
intercell_consensus_filter | 2.327 | 0.136 | 5.351 | |
intercell_generic_categories | 0.117 | 0.000 | 0.117 | |
intercell_network | 0.022 | 0.002 | 0.024 | |
intercell_resources | 0.211 | 0.011 | 0.926 | |
intercell_summary | 0.125 | 0.003 | 0.257 | |
is_ontology_id | 0.000 | 0.000 | 0.001 | |
is_swissprot | 0.083 | 0.002 | 0.170 | |
is_trembl | 0.079 | 0.002 | 0.159 | |
is_uniprot | 0.033 | 0.000 | 0.065 | |
kegg_info | 0.025 | 0.000 | 0.052 | |
kegg_open | 0.023 | 0.000 | 0.050 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.025 | 0.000 | 0.051 | |
kegg_pathway_list | 0.025 | 0.000 | 0.049 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.206 | 0.006 | 5.298 | |
kegg_process | 0.080 | 0.000 | 0.103 | |
latin_name | 0.105 | 0.000 | 0.106 | |
load_db | 0.134 | 0.001 | 0.258 | |
ncbi_taxid | 0.110 | 0.000 | 0.175 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.016 | 0.000 | 0.016 | |
nichenet_gr_network | 0.040 | 0.001 | 0.041 | |
nichenet_gr_network_evex | 0.013 | 0.002 | 0.014 | |
nichenet_gr_network_harmonizome | 0.013 | 0.001 | 0.015 | |
nichenet_gr_network_htridb | 0.014 | 0.000 | 0.014 | |
nichenet_gr_network_omnipath | 17.820 | 0.768 | 24.790 | |
nichenet_gr_network_pathwaycommons | 0.017 | 0.000 | 0.017 | |
nichenet_gr_network_regnetwork | 0.015 | 0.000 | 0.015 | |
nichenet_gr_network_remap | 0.013 | 0.001 | 0.014 | |
nichenet_gr_network_trrust | 0.013 | 0.001 | 0.014 | |
nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.038 | 0.000 | 0.039 | |
nichenet_lr_network_guide2pharma | 0.013 | 0.000 | 0.012 | |
nichenet_lr_network_omnipath | 0.041 | 0.001 | 0.042 | |
nichenet_lr_network_ramilowski | 0.015 | 0.000 | 0.015 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.074 | 0.002 | 0.075 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.045 | 0.001 | 0.045 | |
nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
nichenet_signaling_network | 0.044 | 0.003 | 0.047 | |
nichenet_signaling_network_cpdb | 0.016 | 0.000 | 0.016 | |
nichenet_signaling_network_evex | 0.016 | 0.000 | 0.017 | |
nichenet_signaling_network_harmonizome | 0.017 | 0.000 | 0.017 | |
nichenet_signaling_network_inbiomap | 0.001 | 0.000 | 0.000 | |
nichenet_signaling_network_omnipath | 19.130 | 0.617 | 32.232 | |
nichenet_signaling_network_pathwaycommons | 0.019 | 0.001 | 0.020 | |
nichenet_signaling_network_vinayagam | 0.011 | 0.001 | 0.012 | |
nichenet_test | 0.000 | 0.000 | 0.001 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.122 | 0.004 | 0.184 | |
oma_code | 0.044 | 0.000 | 0.045 | |
oma_organisms | 0.060 | 0.001 | 0.062 | |
oma_pairwise | 0.011 | 0.000 | 0.011 | |
oma_pairwise_genesymbols | 0.009 | 0.000 | 0.009 | |
oma_pairwise_translated | 0.009 | 0.000 | 0.009 | |
omnipath-interactions | 42.926 | 2.016 | 92.080 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.010 | 0.001 | 0.011 | |
omnipath_cache_clean_db | 0.158 | 0.010 | 0.168 | |
omnipath_cache_download_ready | 0.947 | 0.043 | 1.085 | |
omnipath_cache_filter_versions | 0.200 | 0.004 | 0.352 | |
omnipath_cache_get | 0.155 | 0.005 | 0.192 | |
omnipath_cache_key | 0.002 | 0.000 | 0.006 | |
omnipath_cache_latest_or_new | 0.115 | 0.004 | 0.171 | |
omnipath_cache_load | 1.088 | 0.016 | 4.180 | |
omnipath_cache_move_in | 0.286 | 0.014 | 0.504 | |
omnipath_cache_remove | 0.187 | 0.010 | 0.278 | |
omnipath_cache_save | 0.355 | 0.041 | 0.679 | |
omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
omnipath_cache_set_ext | 0.150 | 0.008 | 0.195 | |
omnipath_cache_update_status | 0.203 | 0.034 | 0.236 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0.002 | 0.000 | 0.006 | |
omnipath_for_cosmos | 12.577 | 0.561 | 27.377 | |
omnipath_load_config | 0.001 | 0.000 | 0.001 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.002 | 0.000 | 0.002 | |
omnipath_msg | 0.008 | 0.001 | 0.009 | |
omnipath_query | 6.000 | 0.030 | 6.035 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.052 | 0.002 | 0.054 | |
omnipath_set_console_loglevel | 0.008 | 0.000 | 0.008 | |
omnipath_set_logfile_loglevel | 0.006 | 0.000 | 0.006 | |
omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
omnipath_show_db | 0.134 | 0.000 | 0.134 | |
omnipath_unlock_cache_db | 0.001 | 0.000 | 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 | 0.002 | |
organism_for | 0.144 | 0.001 | 0.145 | |
pathwaycommons_download | 0.002 | 0.000 | 0.002 | |
pivot_annotations | 15.245 | 1.016 | 37.938 | |
preppi_download | 0.000 | 0.001 | 0.002 | |
preppi_filter | 0.001 | 0.000 | 0.002 | |
print_bma_motif_es | 0.402 | 0.058 | 1.408 | |
print_bma_motif_vs | 0.216 | 0.003 | 1.001 | |
print_interactions | 7.140 | 0.299 | 15.688 | |
print_path_es | 0.481 | 0.032 | 2.202 | |
print_path_vs | 1.922 | 0.156 | 4.823 | |
pubmed_open | 3.164 | 0.090 | 3.254 | |
query_info | 0.119 | 0.024 | 0.410 | |
ramilowski_download | 0.001 | 0.000 | 0.001 | |
ramp_id_mapping_table | 0 | 0 | 0 | |
ramp_id_type | 0.001 | 0.002 | 0.003 | |
ramp_sqlite | 0.000 | 0.001 | 0.000 | |
ramp_table | 0.001 | 0.000 | 0.001 | |
ramp_tables | 0.001 | 0.000 | 0.001 | |
regnetwork_directions | 0 | 0 | 0 | |
regnetwork_download | 0 | 0 | 0 | |
relations_list_to_table | 0.090 | 0.013 | 0.138 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.065 | 0.004 | 0.082 | |
remap_dorothea_download | 0 | 0 | 0 | |
remap_filtered | 0.000 | 0.000 | 0.001 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.195 | 0.014 | 0.890 | |
resources | 0.080 | 0.003 | 0.860 | |
resources_colname | 0.581 | 0.058 | 2.868 | |
resources_in | 2.738 | 0.112 | 2.850 | |
show_network | 0.000 | 0.000 | 0.001 | |
signed_ptms | 3.895 | 0.070 | 4.659 | |
simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
static_table | 5.613 | 0.302 | 6.636 | |
static_tables | 0.047 | 0.001 | 0.129 | |
stitch_actions | 0.001 | 0.000 | 0.001 | |
stitch_links | 0.000 | 0.001 | 0.000 | |
stitch_network | 0.000 | 0.001 | 0.000 | |
stitch_remove_prefixes | 0.007 | 0.000 | 0.006 | |
swap_relations | 0.111 | 0.001 | 0.122 | |
swissprots_only | 0.032 | 0.000 | 0.032 | |
tfcensus_download | 0.148 | 0.008 | 0.297 | |
translate_ids | 0.815 | 0.016 | 18.367 | |
translate_ids_multi | 6.011 | 0.177 | 15.454 | |
trembls_only | 0.03 | 0.00 | 0.03 | |
trrust_download | 0.000 | 0.000 | 0.001 | |
uniprot_full_id_mapping_table | 0.678 | 0.053 | 21.588 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0.000 | 0.001 | 0.000 | |
uniprot_id_type | 0.001 | 0.001 | 0.002 | |
uniprot_idmapping_id_types | 0.206 | 0.009 | 0.785 | |
unique_intercell_network | 0.001 | 0.000 | 0.001 | |
unnest_evidences | 0 | 0 | 0 | |
uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
vinayagam_download | 0.001 | 0.000 | 0.001 | |
walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
with_extra_attrs | 7.196 | 0.249 | 9.859 | |
with_references | 0.368 | 0.053 | 1.681 | |
zenodo_download | 0.001 | 0.000 | 0.001 | |