Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
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" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
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: 2024-12-20 03:50:20 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:14:35 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1454.8 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 [2024-12-20 03:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 03:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 03:50:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:42] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 03:50:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 03:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 03:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 03:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 03:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 03:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 03:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 03:50:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:43] [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 [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 03:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 03:50:54] [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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 86.386 0.060 87.883 omnipath-interactions 48.233 4.564 90.657 curated_ligrec_stats 29.345 1.054 100.238 nichenet_signaling_network_omnipath 17.005 0.783 28.329 filter_extra_attrs 14.293 0.169 15.164 translate_ids_multi 13.175 0.565 30.380 pivot_annotations 11.419 1.041 21.152 omnipath_for_cosmos 10.298 0.752 24.848 static_table 9.906 0.669 23.317 nichenet_gr_network_omnipath 9.976 0.493 12.673 print_interactions 9.528 0.585 17.700 go_annot_download 9.361 0.696 9.950 with_extra_attrs 9.154 0.610 12.767 extra_attr_values 9.285 0.203 12.125 giant_component 7.881 0.382 11.170 extra_attrs_to_cols 7.858 0.149 8.008 omnipath_query 7.110 0.174 7.314 signed_ptms 6.725 0.317 9.301 pubmed_open 5.764 0.188 5.982 filter_by_resource 5.129 0.238 7.877 extra_attrs 5.324 0.017 5.340 has_extra_attrs 5.123 0.112 5.236 filter_intercell 4.849 0.328 8.923 curated_ligand_receptor_interactions 4.466 0.333 14.062 print_path_vs 3.644 0.351 6.610 translate_ids 2.374 0.188 21.108 uniprot_full_id_mapping_table 1.425 0.090 23.363 ensembl_id_mapping_table 1.114 0.057 10.840 all_uniprots 0.855 0.054 19.752 * 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 [2024-12-19 15:32:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Contains 6 files. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:32:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 15:32:59] [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). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [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). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [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). [2024-12-19 15:32:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:32:59] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 15:33:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 15:33:01] [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) [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Contains 21 files. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 04:03:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:03:29] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 10.842 0.822 40.040
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0.001 | 0.000 | 0.000 | |
all_uniprot_acs | 0.014 | 0.002 | 0.016 | |
all_uniprots | 0.855 | 0.054 | 19.752 | |
ancestors | 0.007 | 0.000 | 0.008 | |
annotated_network | 0.844 | 0.119 | 3.855 | |
annotation_categories | 86.386 | 0.060 | 87.883 | |
annotation_resources | 0.107 | 0.010 | 0.802 | |
annotations | 0.337 | 0.026 | 1.185 | |
biomart_query | 0.715 | 0.050 | 3.224 | |
bioplex1 | 0.006 | 0.001 | 0.008 | |
bioplex2 | 0.007 | 0.000 | 0.007 | |
bioplex3 | 0.037 | 0.000 | 0.037 | |
bioplex_all | 0.006 | 0.002 | 0.007 | |
bioplex_hct116_1 | 0.005 | 0.002 | 0.008 | |
bma_motif_es | 0.364 | 0.037 | 1.504 | |
bma_motif_vs | 0.184 | 0.001 | 0.950 | |
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 | 0.007 | 0.000 | 0.007 | |
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 | 0.052 | 0.000 | 0.053 | |
complex_genes | 0.444 | 0.013 | 2.181 | |
complex_resources | 0.144 | 0.002 | 0.844 | |
complexes | 0.189 | 0.001 | 0.821 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.007 | 0.000 | 0.007 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 4.466 | 0.333 | 14.062 | |
curated_ligrec_stats | 29.345 | 1.054 | 100.238 | |
database_summary | 1.300 | 0.015 | 3.851 | |
descendants | 0.023 | 0.000 | 0.023 | |
ensembl_dataset | 0.012 | 0.000 | 0.012 | |
ensembl_id_mapping_table | 1.114 | 0.057 | 10.840 | |
ensembl_id_type | 0.001 | 0.001 | 0.003 | |
ensembl_name | 0.055 | 0.001 | 0.056 | |
ensembl_organisms | 0.095 | 0.002 | 0.097 | |
ensembl_organisms_raw | 0.114 | 0.004 | 0.118 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 1.947 | 0.038 | 4.204 | |
enzsub_resources | 0.111 | 0.002 | 0.665 | |
enzyme_substrate | 1.229 | 0.004 | 1.960 | |
evex_download | 0.011 | 0.000 | 0.012 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 9.285 | 0.203 | 12.125 | |
extra_attrs | 5.324 | 0.017 | 5.340 | |
extra_attrs_to_cols | 7.858 | 0.149 | 8.008 | |
filter_by_resource | 5.129 | 0.238 | 7.877 | |
filter_extra_attrs | 14.293 | 0.169 | 15.164 | |
filter_intercell | 4.849 | 0.328 | 8.923 | |
filter_intercell_network | 0.015 | 0.000 | 0.015 | |
find_all_paths | 4.561 | 0.053 | 4.613 | |
from_evidences | 0 | 0 | 0 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.008 | 0.000 | 0.008 | |
giant_component | 7.881 | 0.382 | 11.170 | |
go_annot_download | 9.361 | 0.696 | 9.950 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.007 | 0.000 | 0.007 | |
guide2pharma_download | 0.006 | 0.001 | 0.007 | |
harmonizome_download | 0.007 | 0.000 | 0.006 | |
has_extra_attrs | 5.123 | 0.112 | 5.236 | |
hmdb_id_mapping_table | 0.007 | 0.000 | 0.007 | |
hmdb_id_type | 0.002 | 0.000 | 0.002 | |
hmdb_metabolite_fields | 0.001 | 0.000 | 0.000 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.007 | 0.000 | 0.008 | |
homologene_download | 0.007 | 0.000 | 0.007 | |
homologene_raw | 0.019 | 0.001 | 0.020 | |
homologene_uniprot_orthology | 0.008 | 0.000 | 0.008 | |
hpo_download | 1.855 | 0.206 | 2.414 | |
htridb_download | 0.007 | 0.002 | 0.009 | |
id_translation_resources | 0.000 | 0.000 | 0.001 | |
id_types | 0.037 | 0.004 | 0.041 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.443 | 0.029 | 0.855 | |
interaction_graph | 0.347 | 0.052 | 0.954 | |
interaction_resources | 0.146 | 0.004 | 0.786 | |
interaction_types | 0.041 | 0.003 | 0.044 | |
intercell | 0.377 | 0.069 | 0.914 | |
intercell_categories | 0.303 | 0.021 | 0.519 | |
intercell_consensus_filter | 0.984 | 0.170 | 2.841 | |
intercell_generic_categories | 0.042 | 0.003 | 0.045 | |
intercell_network | 0.007 | 0.002 | 0.009 | |
intercell_resources | 0.126 | 0.008 | 0.823 | |
intercell_summary | 0.041 | 0.002 | 0.043 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.024 | 0.000 | 0.024 | |
is_trembl | 0.021 | 0.001 | 0.023 | |
is_uniprot | 0.008 | 0.000 | 0.008 | |
kegg_info | 0.006 | 0.000 | 0.007 | |
kegg_open | 0.007 | 0.000 | 0.007 | |
kegg_pathway_annotations | 0.001 | 0.000 | 0.000 | |
kegg_pathway_download | 0.007 | 0.000 | 0.007 | |
kegg_pathway_list | 0.007 | 0.000 | 0.007 | |
kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
kegg_picture | 0.136 | 0.005 | 3.994 | |
kegg_process | 0.022 | 0.000 | 0.022 | |
latin_name | 0.084 | 0.000 | 0.085 | |
load_db | 0.065 | 0.017 | 0.084 | |
ncbi_taxid | 0.057 | 0.006 | 0.063 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.006 | 0.005 | 0.011 | |
nichenet_gr_network | 0.022 | 0.002 | 0.024 | |
nichenet_gr_network_evex | 0.007 | 0.001 | 0.008 | |
nichenet_gr_network_harmonizome | 0.007 | 0.001 | 0.008 | |
nichenet_gr_network_htridb | 0.006 | 0.002 | 0.008 | |
nichenet_gr_network_omnipath | 9.976 | 0.493 | 12.673 | |
nichenet_gr_network_pathwaycommons | 0.009 | 0.000 | 0.009 | |
nichenet_gr_network_regnetwork | 0.006 | 0.001 | 0.008 | |
nichenet_gr_network_remap | 0.007 | 0.000 | 0.008 | |
nichenet_gr_network_trrust | 0.008 | 0.000 | 0.007 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.021 | 0.000 | 0.022 | |
nichenet_lr_network_guide2pharma | 0.007 | 0.001 | 0.008 | |
nichenet_lr_network_omnipath | 0.022 | 0.003 | 0.025 | |
nichenet_lr_network_ramilowski | 0.006 | 0.002 | 0.008 | |
nichenet_main | 0.001 | 0.000 | 0.000 | |
nichenet_networks | 0.036 | 0.000 | 0.036 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.020 | 0.001 | 0.021 | |
nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
nichenet_signaling_network | 0.021 | 0.001 | 0.022 | |
nichenet_signaling_network_cpdb | 0.007 | 0.000 | 0.008 | |
nichenet_signaling_network_evex | 0.006 | 0.001 | 0.008 | |
nichenet_signaling_network_harmonizome | 0.007 | 0.001 | 0.008 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 17.005 | 0.783 | 28.329 | |
nichenet_signaling_network_pathwaycommons | 0.039 | 0.001 | 0.082 | |
nichenet_signaling_network_vinayagam | 0.031 | 0.000 | 0.062 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.314 | 0.005 | 0.841 | |
oma_code | 0.117 | 0.001 | 0.236 | |
oma_organisms | 0.167 | 0.002 | 0.181 | |
oma_pairwise | 0.034 | 0.000 | 0.034 | |
oma_pairwise_genesymbols | 0.041 | 0.002 | 0.083 | |
oma_pairwise_translated | 0.048 | 0.000 | 0.094 | |
omnipath-interactions | 48.233 | 4.564 | 90.657 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.004 | 0.002 | 0.006 | |
omnipath_cache_clean_db | 0.073 | 0.007 | 0.080 | |
omnipath_cache_download_ready | 0.482 | 0.079 | 0.568 | |
omnipath_cache_filter_versions | 0.086 | 0.003 | 0.094 | |
omnipath_cache_get | 0.064 | 0.003 | 0.067 | |
omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
omnipath_cache_latest_or_new | 0.071 | 0.005 | 0.076 | |
omnipath_cache_load | 0.749 | 0.063 | 3.479 | |
omnipath_cache_move_in | 0.120 | 0.014 | 0.137 | |
omnipath_cache_remove | 0.075 | 0.006 | 0.085 | |
omnipath_cache_save | 0.161 | 0.019 | 0.289 | |
omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
omnipath_cache_set_ext | 0.056 | 0.009 | 0.068 | |
omnipath_cache_update_status | 0.083 | 0.016 | 0.099 | |
omnipath_cache_wipe | 0.001 | 0.000 | 0.000 | |
omnipath_config_path | 0.000 | 0.000 | 0.001 | |
omnipath_for_cosmos | 10.298 | 0.752 | 24.848 | |
omnipath_load_config | 0 | 0 | 0 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.004 | 0.000 | 0.003 | |
omnipath_msg | 0.010 | 0.001 | 0.012 | |
omnipath_query | 7.110 | 0.174 | 7.314 | |
omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
omnipath_save_config | 0.001 | 0.000 | 0.000 | |
omnipath_set_cachedir | 0.055 | 0.001 | 0.056 | |
omnipath_set_console_loglevel | 0.008 | 0.000 | 0.008 | |
omnipath_set_logfile_loglevel | 0.007 | 0.000 | 0.006 | |
omnipath_set_loglevel | 0.004 | 0.000 | 0.003 | |
omnipath_show_db | 0.139 | 0.000 | 0.160 | |
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 | 0.001 | 0.001 | 0.002 | |
organism_for | 0.117 | 0.001 | 0.181 | |
pathwaycommons_download | 0.001 | 0.000 | 0.002 | |
pivot_annotations | 11.419 | 1.041 | 21.152 | |
preppi_download | 0.001 | 0.000 | 0.001 | |
preppi_filter | 0.000 | 0.001 | 0.001 | |
print_bma_motif_es | 0.540 | 0.101 | 1.751 | |
print_bma_motif_vs | 0.296 | 0.008 | 1.319 | |
print_interactions | 9.528 | 0.585 | 17.700 | |
print_path_es | 0.942 | 0.104 | 2.956 | |
print_path_vs | 3.644 | 0.351 | 6.610 | |
pubmed_open | 5.764 | 0.188 | 5.982 | |
query_info | 0.204 | 0.011 | 0.508 | |
ramilowski_download | 0.001 | 0.000 | 0.001 | |
ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
ramp_id_type | 0.004 | 0.000 | 0.009 | |
ramp_sqlite | 0.001 | 0.000 | 0.001 | |
ramp_table | 0.001 | 0.000 | 0.000 | |
ramp_tables | 0.000 | 0.000 | 0.001 | |
regnetwork_directions | 0.001 | 0.000 | 0.001 | |
regnetwork_download | 0.000 | 0.000 | 0.001 | |
relations_list_to_table | 0.130 | 0.004 | 0.201 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.110 | 0.008 | 0.133 | |
remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
remap_filtered | 0 | 0 | 0 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.271 | 0.023 | 0.929 | |
resources | 0.156 | 0.006 | 0.705 | |
resources_colname | 0.895 | 0.075 | 2.911 | |
resources_in | 3.369 | 0.146 | 3.516 | |
show_network | 0.000 | 0.000 | 0.001 | |
signed_ptms | 6.725 | 0.317 | 9.301 | |
simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
static_table | 9.906 | 0.669 | 23.317 | |
static_tables | 0.113 | 0.013 | 0.157 | |
stitch_actions | 0.002 | 0.000 | 0.006 | |
stitch_links | 0.001 | 0.000 | 0.001 | |
stitch_network | 0.001 | 0.001 | 0.002 | |
stitch_remove_prefixes | 0.017 | 0.000 | 0.017 | |
swap_relations | 0.350 | 0.006 | 0.630 | |
swissprots_only | 0.087 | 0.031 | 0.118 | |
tfcensus_download | 0.347 | 0.037 | 0.568 | |
translate_ids | 2.374 | 0.188 | 21.108 | |
translate_ids_multi | 13.175 | 0.565 | 30.380 | |
trembls_only | 0.074 | 0.001 | 0.192 | |
trrust_download | 0.001 | 0.000 | 0.005 | |
uniprot_full_id_mapping_table | 1.425 | 0.090 | 23.363 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0.001 | 0.001 | 0.001 | |
uniprot_id_type | 0.003 | 0.000 | 0.003 | |
uniprot_idmapping_id_types | 0.356 | 0.041 | 1.162 | |
unique_intercell_network | 0.001 | 0.001 | 0.002 | |
unnest_evidences | 0 | 0 | 0 | |
uploadlists_id_type | 0.004 | 0.000 | 0.004 | |
vinayagam_download | 0.001 | 0.000 | 0.001 | |
walk_ontology_tree | 0.002 | 0.000 | 0.002 | |
with_extra_attrs | 9.154 | 0.610 | 12.767 | |
with_references | 0.413 | 0.076 | 2.126 | |
zenodo_download | 0.001 | 0.000 | 0.001 | |