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 12:05 -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: 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_3.14.0.tar.gz |
StartedAt: 2024-12-20 04:16:49 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:30:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 824.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OmnipathR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '3.14.0' * 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 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 whether startup messages can be suppressed ... NOTE [2024-12-20 04:17:22] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:22] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 04:17:22] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:22] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 04:17:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 04:17:22] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:22] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:23] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 04:17:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 04:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 04:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 04:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:23] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 04:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:23] [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 04:17:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 04:17:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 04:17:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:17:41] [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 70.81 0.06 71.52 omnipath-interactions 32.48 1.48 85.06 curated_ligrec_stats 31.58 1.54 77.24 filter_extra_attrs 20.99 0.16 21.58 nichenet_gr_network_omnipath 13.91 0.80 15.22 go_annot_download 11.92 0.85 11.44 pivot_annotations 11.28 0.95 29.89 nichenet_signaling_network_omnipath 11.12 0.83 13.13 extra_attr_values 11.72 0.19 12.61 extra_attrs_to_cols 11.55 0.08 11.63 giant_component 10.46 0.40 11.28 omnipath_for_cosmos 10.38 0.22 21.22 with_extra_attrs 9.92 0.33 10.67 translate_ids_multi 7.30 0.19 17.13 extra_attrs 6.92 0.04 7.03 static_table 6.58 0.30 7.31 print_interactions 6.53 0.28 13.97 filter_intercell 6.35 0.38 6.62 filter_by_resource 6.45 0.17 7.22 has_extra_attrs 6.44 0.03 6.47 find_all_paths 5.58 0.06 5.64 curated_ligand_receptor_interactions 5.03 0.38 11.90 signed_ptms 4.98 0.00 5.49 ensembl_id_mapping_table 1.77 0.11 12.07 translate_ids 1.15 0.12 18.47 uniprot_full_id_mapping_table 1.11 0.13 22.39 all_uniprots 0.76 0.12 20.58 print_path_es 0.58 0.11 9.90 print_bma_motif_es 0.30 0.11 5.67 * 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: 2 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 [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 16:16:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:38] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-12-19 16:16:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:40] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 16:16:40] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:41] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 16:16:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 16:16:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:41] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 16:16:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 16:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 16:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 16:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:41] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 16:16:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:41] [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 ucrt) -- "Pile of Leaves" 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) [2024-12-20 04:29:38] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:38] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Contains 21 files. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 04:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:38] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 04:29:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 04:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:38] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 04:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:39] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 04:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:39] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 04:29:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 04:29:39] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 11.79 1.21 32.73
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.03 | 0.00 | 0.03 | |
all_uniprots | 0.76 | 0.12 | 20.58 | |
ancestors | 0.02 | 0.00 | 0.01 | |
annotated_network | 0.92 | 0.10 | 3.03 | |
annotation_categories | 70.81 | 0.06 | 71.52 | |
annotation_resources | 0.08 | 0.00 | 0.48 | |
annotations | 0.32 | 0.03 | 1.05 | |
biomart_query | 1.14 | 0.06 | 3.13 | |
bioplex1 | 0.01 | 0.00 | 0.01 | |
bioplex2 | 0.02 | 0.00 | 0.02 | |
bioplex3 | 0.01 | 0.00 | 0.01 | |
bioplex_all | 0.07 | 0.00 | 0.08 | |
bioplex_hct116_1 | 0 | 0 | 0 | |
bma_motif_es | 0.35 | 0.06 | 1.17 | |
bma_motif_vs | 0.22 | 0.00 | 0.61 | |
chalmers_gem | 0.01 | 0.00 | 0.01 | |
chalmers_gem_id_mapping_table | 0 | 0 | 0 | |
chalmers_gem_id_type | 0.02 | 0.00 | 0.02 | |
chalmers_gem_metabolites | 0 | 0 | 0 | |
chalmers_gem_network | 0.02 | 0.00 | 0.01 | |
chalmers_gem_raw | 0.01 | 0.00 | 0.02 | |
chalmers_gem_reactions | 0.02 | 0.00 | 0.02 | |
common_name | 0.03 | 0.00 | 0.03 | |
complex_genes | 0.59 | 0.05 | 1.73 | |
complex_resources | 0.05 | 0.00 | 0.72 | |
complexes | 0.23 | 0.00 | 0.64 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.02 | 0.00 | 0.02 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 5.03 | 0.38 | 11.90 | |
curated_ligrec_stats | 31.58 | 1.54 | 77.24 | |
database_summary | 1.53 | 0.03 | 2.33 | |
descendants | 0.02 | 0.00 | 0.01 | |
ensembl_dataset | 0.01 | 0.00 | 0.02 | |
ensembl_id_mapping_table | 1.77 | 0.11 | 12.07 | |
ensembl_id_type | 0 | 0 | 0 | |
ensembl_name | 0.09 | 0.00 | 0.10 | |
ensembl_organisms | 0.16 | 0.00 | 0.15 | |
ensembl_organisms_raw | 0.25 | 0.03 | 0.29 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.36 | 0.10 | 3.50 | |
enzsub_resources | 0.06 | 0.01 | 0.48 | |
enzyme_substrate | 0.90 | 0.02 | 1.33 | |
evex_download | 0.02 | 0.00 | 0.01 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 11.72 | 0.19 | 12.61 | |
extra_attrs | 6.92 | 0.04 | 7.03 | |
extra_attrs_to_cols | 11.55 | 0.08 | 11.63 | |
filter_by_resource | 6.45 | 0.17 | 7.22 | |
filter_extra_attrs | 20.99 | 0.16 | 21.58 | |
filter_intercell | 6.35 | 0.38 | 6.62 | |
filter_intercell_network | 0.02 | 0.00 | 0.02 | |
find_all_paths | 5.58 | 0.06 | 5.64 | |
from_evidences | 0 | 0 | 0 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.01 | 0.00 | 0.01 | |
giant_component | 10.46 | 0.40 | 11.28 | |
go_annot_download | 11.92 | 0.85 | 11.44 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.01 | 0.00 | 0.02 | |
guide2pharma_download | 0 | 0 | 0 | |
harmonizome_download | 0 | 0 | 0 | |
has_extra_attrs | 6.44 | 0.03 | 6.47 | |
hmdb_id_mapping_table | 0.02 | 0.00 | 0.02 | |
hmdb_id_type | 0 | 0 | 0 | |
hmdb_metabolite_fields | 0 | 0 | 0 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.01 | 0.00 | 0.01 | |
homologene_download | 0 | 0 | 0 | |
homologene_raw | 0.02 | 0.00 | 0.02 | |
homologene_uniprot_orthology | 0.01 | 0.00 | 0.01 | |
hpo_download | 1.77 | 0.21 | 2.19 | |
htridb_download | 0.02 | 0.00 | 0.02 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.03 | 0.00 | 0.03 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.45 | 0.01 | 0.94 | |
interaction_graph | 0.39 | 0.03 | 0.84 | |
interaction_resources | 0.06 | 0.00 | 0.47 | |
interaction_types | 0.07 | 0.00 | 0.06 | |
intercell | 0.50 | 0.05 | 1.02 | |
intercell_categories | 0.36 | 0.03 | 0.70 | |
intercell_consensus_filter | 1.42 | 0.24 | 2.22 | |
intercell_generic_categories | 0.06 | 0.00 | 0.06 | |
intercell_network | 0.02 | 0.00 | 0.02 | |
intercell_resources | 0.12 | 0.00 | 0.53 | |
intercell_summary | 0.05 | 0.01 | 0.06 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.04 | 0.00 | 0.05 | |
is_trembl | 0.04 | 0.00 | 0.03 | |
is_uniprot | 0.01 | 0.00 | 0.01 | |
kegg_info | 0.02 | 0.00 | 0.02 | |
kegg_open | 0 | 0 | 0 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.02 | 0.00 | 0.01 | |
kegg_pathway_list | 0.01 | 0.00 | 0.02 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.10 | 0.00 | 2.64 | |
kegg_process | 0.03 | 0.00 | 0.03 | |
latin_name | 0.08 | 0.00 | 0.08 | |
load_db | 0.09 | 0.02 | 0.11 | |
ncbi_taxid | 0.14 | 0.00 | 0.14 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.02 | 0.00 | 0.01 | |
nichenet_gr_network | 0.04 | 0.00 | 0.05 | |
nichenet_gr_network_evex | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_harmonizome | 0.01 | 0.00 | 0.01 | |
nichenet_gr_network_htridb | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_omnipath | 13.91 | 0.80 | 15.22 | |
nichenet_gr_network_pathwaycommons | 0 | 0 | 0 | |
nichenet_gr_network_regnetwork | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_remap | 0.01 | 0.00 | 0.01 | |
nichenet_gr_network_trrust | 0.02 | 0.00 | 0.02 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.08 | 0.01 | 0.09 | |
nichenet_lr_network_guide2pharma | 0 | 0 | 0 | |
nichenet_lr_network_omnipath | 0.03 | 0.00 | 0.03 | |
nichenet_lr_network_ramilowski | 0 | 0 | 0 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.05 | 0.00 | 0.05 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.05 | 0.00 | 0.04 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.03 | 0.00 | 0.03 | |
nichenet_signaling_network_cpdb | 0.01 | 0.00 | 0.02 | |
nichenet_signaling_network_evex | 0.02 | 0.00 | 0.01 | |
nichenet_signaling_network_harmonizome | 0.02 | 0.00 | 0.02 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 11.12 | 0.83 | 13.13 | |
nichenet_signaling_network_pathwaycommons | 0.02 | 0.00 | 0.01 | |
nichenet_signaling_network_vinayagam | 0.01 | 0.00 | 0.02 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.13 | 0.01 | 0.29 | |
oma_code | 0.04 | 0.00 | 0.05 | |
oma_organisms | 0.13 | 0.00 | 0.12 | |
oma_pairwise | 0.01 | 0.00 | 0.02 | |
oma_pairwise_genesymbols | 0.02 | 0.00 | 0.01 | |
oma_pairwise_translated | 0.02 | 0.00 | 0.02 | |
omnipath-interactions | 32.48 | 1.48 | 85.06 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0 | 0 | 0 | |
omnipath_cache_clean_db | 0.15 | 0.00 | 0.15 | |
omnipath_cache_download_ready | 0.74 | 0.07 | 2.22 | |
omnipath_cache_filter_versions | 0.15 | 0.01 | 0.80 | |
omnipath_cache_get | 0.11 | 0.05 | 0.36 | |
omnipath_cache_key | 0 | 0 | 0 | |
omnipath_cache_latest_or_new | 0.10 | 0.02 | 0.11 | |
omnipath_cache_load | 0.62 | 0.06 | 2.17 | |
omnipath_cache_move_in | 0.3 | 0.0 | 0.5 | |
omnipath_cache_remove | 0.18 | 0.01 | 0.27 | |
omnipath_cache_save | 0.18 | 0.05 | 0.42 | |
omnipath_cache_search | 0 | 0 | 0 | |
omnipath_cache_set_ext | 0.14 | 0.05 | 0.30 | |
omnipath_cache_update_status | 0.14 | 0.01 | 0.17 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0 | 0 | 0 | |
omnipath_for_cosmos | 10.38 | 0.22 | 21.22 | |
omnipath_load_config | 0 | 0 | 0 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0 | 0 | 0 | |
omnipath_msg | 0.01 | 0.00 | 0.01 | |
omnipath_query | 3.63 | 0.00 | 3.63 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.05 | 0.00 | 0.05 | |
omnipath_set_console_loglevel | 0 | 0 | 0 | |
omnipath_set_logfile_loglevel | 0 | 0 | 0 | |
omnipath_set_loglevel | 0 | 0 | 0 | |
omnipath_show_db | 0.05 | 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 | |
organism_for | 0.09 | 0.00 | 0.10 | |
pathwaycommons_download | 0 | 0 | 0 | |
pivot_annotations | 11.28 | 0.95 | 29.89 | |
preppi_download | 0 | 0 | 0 | |
preppi_filter | 0 | 0 | 0 | |
print_bma_motif_es | 0.30 | 0.11 | 5.67 | |
print_bma_motif_vs | 0.17 | 0.00 | 1.08 | |
print_interactions | 6.53 | 0.28 | 13.97 | |
print_path_es | 0.58 | 0.11 | 9.90 | |
print_path_vs | 2.38 | 0.09 | 4.19 | |
pubmed_open | 4.43 | 0.00 | 4.50 | |
query_info | 0.10 | 0.02 | 0.64 | |
ramilowski_download | 0.0 | 0.0 | 0.1 | |
ramp_id_mapping_table | 0 | 0 | 0 | |
ramp_id_type | 0.00 | 0.00 | 0.01 | |
ramp_sqlite | 0 | 0 | 0 | |
ramp_table | 0 | 0 | 0 | |
ramp_tables | 0 | 0 | 0 | |
regnetwork_directions | 0 | 0 | 0 | |
regnetwork_download | 0 | 0 | 0 | |
relations_list_to_table | 0.13 | 0.00 | 0.33 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.08 | 0.02 | 0.22 | |
remap_dorothea_download | 0.01 | 0.00 | 0.01 | |
remap_filtered | 0 | 0 | 0 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.63 | 0.03 | 1.52 | |
resources | 0.04 | 0.00 | 0.77 | |
resources_colname | 0.71 | 0.04 | 4.50 | |
resources_in | 3.86 | 0.03 | 3.90 | |
show_network | 0 | 0 | 0 | |
signed_ptms | 4.98 | 0.00 | 5.49 | |
simplify_intercell_network | 0 | 0 | 0 | |
static_table | 6.58 | 0.30 | 7.31 | |
static_tables | 0.06 | 0.00 | 0.14 | |
stitch_actions | 0 | 0 | 0 | |
stitch_links | 0 | 0 | 0 | |
stitch_network | 0 | 0 | 0 | |
stitch_remove_prefixes | 0.01 | 0.00 | 0.02 | |
swap_relations | 0.18 | 0.02 | 0.20 | |
swissprots_only | 0.04 | 0.00 | 0.05 | |
tfcensus_download | 0.21 | 0.00 | 0.28 | |
translate_ids | 1.15 | 0.12 | 18.47 | |
translate_ids_multi | 7.30 | 0.19 | 17.13 | |
trembls_only | 0.03 | 0.02 | 0.04 | |
trrust_download | 0 | 0 | 0 | |
uniprot_full_id_mapping_table | 1.11 | 0.13 | 22.39 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0 | 0 | 0 | |
uniprot_id_type | 0 | 0 | 0 | |
uniprot_idmapping_id_types | 0.20 | 0.01 | 0.56 | |
unique_intercell_network | 0 | 0 | 0 | |
unnest_evidences | 0 | 0 | 0 | |
uploadlists_id_type | 0 | 0 | 0 | |
vinayagam_download | 0 | 0 | 0 | |
walk_ontology_tree | 0.02 | 0.00 | 0.02 | |
with_extra_attrs | 9.92 | 0.33 | 10.67 | |
with_references | 0.59 | 0.08 | 1.72 | |
zenodo_download | 0 | 0 | 0 | |