Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 1413/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.7.15 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: OmnipathR |
Version: 3.7.15 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz |
StartedAt: 2023-04-11 22:05:58 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 22:35:04 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 1745.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OmnipathR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.7.15’ * 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 R 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 startup messages can be suppressed ... NOTE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [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 [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [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 65.143 0.076 66.660 curated_ligrec_stats 34.484 1.579 111.639 extra_attrs_to_cols 32.840 0.052 37.548 filter_extra_attrs 31.392 0.280 37.606 extra_attr_values 26.131 0.312 30.136 with_extra_attrs 24.587 0.499 41.532 go_annot_download 20.076 1.192 33.236 giant_component 19.603 0.989 31.496 has_extra_attrs 19.901 0.169 31.165 pivot_annotations 17.280 1.644 42.469 nichenet_gr_network_omnipath 17.306 0.534 21.776 extra_attrs 14.376 0.111 16.150 get_signed_ptms 12.614 0.202 24.519 nichenet_signaling_network_omnipath 10.390 0.803 26.226 print_interactions 9.932 0.462 19.328 filter_intercell 9.539 0.600 15.078 pubmed_open 8.698 0.561 18.925 filter_by_resource 8.427 0.272 11.372 find_all_paths 6.120 0.091 6.211 curated_ligand_receptor_interactions 5.634 0.281 16.096 omnipath 4.675 0.384 6.187 print_path_vs 4.459 0.340 11.195 import_all_interactions 3.844 0.207 8.669 collectri 3.909 0.111 5.779 import_transcriptional_interactions 3.799 0.198 10.158 omnipath_cache_download_ready 0.651 3.002 6.299 database_summary 1.760 1.291 5.538 import_kinaseextra_interactions 2.663 0.259 5.815 hpo_download 2.618 0.214 6.125 omnipath_cache_load 0.704 1.787 12.748 import_mirnatarget_interactions 2.113 0.205 5.889 intercell_consensus_filter 2.121 0.159 5.512 obo_parser 0.169 1.264 19.885 annotated_network 1.214 0.147 5.140 ensembl_id_mapping_table 1.217 0.037 15.624 biomart_query 1.175 0.045 5.893 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Contains 6 files. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 15:24:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:33] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 15:24:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:34] [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 4.3.0 alpha (2023-04-03 r84154) Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) 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 > # 2018-2023 > # 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) [2023-04-11 22:21:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:21:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:21:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 22:21:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:21:26] [TRACE] [OmnipathR] Contains 15 files. [2023-04-11 22:21:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 22:21:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:21:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:21:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 22:21:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 22:21:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 22:21:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 22:21:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 22:21:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:21:27] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 21.695 1.523 64.902
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0.001 | 0.000 | 0.001 | |
all_uniprot_acs | 0.024 | 0.000 | 0.024 | |
all_uniprots | 0.011 | 0.000 | 0.011 | |
ancestors | 0.01 | 0.00 | 0.01 | |
annotated_network | 1.214 | 0.147 | 5.140 | |
annotation_categories | 65.143 | 0.076 | 66.660 | |
biomart_query | 1.175 | 0.045 | 5.893 | |
bioplex1 | 0.010 | 0.008 | 0.018 | |
bioplex2 | 0.015 | 0.000 | 0.015 | |
bioplex3 | 0.015 | 0.000 | 0.015 | |
bioplex_all | 0.008 | 0.004 | 0.013 | |
bioplex_hct116_1 | 0.011 | 0.000 | 0.011 | |
bma_motif_es | 0.479 | 0.028 | 1.416 | |
bma_motif_vs | 0.260 | 0.004 | 1.020 | |
collectri | 3.909 | 0.111 | 5.779 | |
common_name | 0.032 | 0.000 | 0.032 | |
consensuspathdb_download | 0.001 | 0.000 | 0.001 | |
consensuspathdb_raw_table | 0.010 | 0.004 | 0.013 | |
curated_ligand_receptor_interactions | 5.634 | 0.281 | 16.096 | |
curated_ligrec_stats | 34.484 | 1.579 | 111.639 | |
database_summary | 1.760 | 1.291 | 5.538 | |
descendants | 0.013 | 0.004 | 0.016 | |
dorothea | 2.274 | 0.053 | 4.283 | |
ensembl_dataset | 0.012 | 0.000 | 0.013 | |
ensembl_id_mapping_table | 1.217 | 0.037 | 15.624 | |
ensembl_id_type | 0.006 | 0.000 | 0.007 | |
ensembl_name | 0.06 | 0.00 | 0.06 | |
ensembl_organisms | 0.245 | 0.011 | 0.256 | |
ensembl_organisms_raw | 0.275 | 0.000 | 0.294 | |
ensembl_orthology | 0.000 | 0.001 | 0.000 | |
enzsub_graph | 2.363 | 0.138 | 4.609 | |
evex_download | 0.011 | 0.000 | 0.010 | |
extra_attr_values | 26.131 | 0.312 | 30.136 | |
extra_attrs | 14.376 | 0.111 | 16.150 | |
extra_attrs_to_cols | 32.840 | 0.052 | 37.548 | |
filter_by_resource | 8.427 | 0.272 | 11.372 | |
filter_extra_attrs | 31.392 | 0.280 | 37.606 | |
filter_intercell | 9.539 | 0.600 | 15.078 | |
filter_intercell_network | 0.033 | 0.000 | 0.034 | |
find_all_paths | 6.120 | 0.091 | 6.211 | |
get_annotation_resources | 0.191 | 0.008 | 0.882 | |
get_complex_genes | 1.351 | 0.061 | 3.325 | |
get_complex_resources | 0.172 | 0.004 | 1.049 | |
get_db | 0.000 | 0.000 | 0.001 | |
get_enzsub_resources | 0.294 | 0.044 | 1.191 | |
get_interaction_resources | 0.211 | 0.008 | 1.191 | |
get_intercell_categories | 0.551 | 0.052 | 1.044 | |
get_intercell_generic_categories | 0.040 | 0.004 | 0.043 | |
get_intercell_resources | 0.276 | 0.016 | 1.326 | |
get_ontology_db | 0.021 | 0.004 | 0.040 | |
get_resources | 0.197 | 0.008 | 1.060 | |
get_signed_ptms | 12.614 | 0.202 | 24.519 | |
giant_component | 19.603 | 0.989 | 31.496 | |
go_annot_download | 20.076 | 1.192 | 33.236 | |
go_annot_slim | 0.000 | 0.001 | 0.001 | |
go_ontology_download | 0.016 | 0.003 | 0.018 | |
guide2pharma_download | 0.015 | 0.003 | 0.018 | |
harmonizome_download | 0.019 | 0.000 | 0.019 | |
has_extra_attrs | 19.901 | 0.169 | 31.165 | |
homologene_download | 0.029 | 0.004 | 0.084 | |
homologene_raw | 0.057 | 0.004 | 0.136 | |
homologene_uniprot_orthology | 0.028 | 0.004 | 0.064 | |
homology_translate | 0.000 | 0.000 | 0.001 | |
hpo_download | 2.618 | 0.214 | 6.125 | |
htridb_download | 0.035 | 0.000 | 0.035 | |
import_all_interactions | 3.844 | 0.207 | 8.669 | |
import_intercell_network | 0.027 | 0.000 | 0.028 | |
import_kinaseextra_interactions | 2.663 | 0.259 | 5.815 | |
import_ligrecextra_interactions | 1.424 | 0.115 | 3.697 | |
import_lncrna_mrna_interactions | 1.010 | 0.115 | 2.888 | |
import_mirnatarget_interactions | 2.113 | 0.205 | 5.889 | |
import_omnipath_annotations | 1.120 | 0.085 | 2.627 | |
import_omnipath_complexes | 1.040 | 0.076 | 3.285 | |
import_omnipath_enzsub | 1.389 | 0.028 | 2.092 | |
import_omnipath_interactions | 0.451 | 0.061 | 1.248 | |
import_omnipath_intercell | 0.471 | 0.044 | 1.040 | |
import_pathwayextra_interactions | 1.360 | 0.146 | 3.458 | |
import_post_translational_interactions | 1.574 | 0.114 | 4.106 | |
import_small_molecule_protein_interactions | 0.842 | 0.101 | 1.304 | |
import_tf_mirna_interactions | 1.358 | 0.102 | 2.894 | |
import_tf_target_interactions | 2.027 | 0.140 | 4.251 | |
import_transcriptional_interactions | 3.799 | 0.198 | 10.158 | |
inbiomap_download | 0.001 | 0.000 | 0.001 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 1.147 | 0.036 | 1.956 | |
interaction_graph | 0.639 | 0.053 | 2.077 | |
interaction_types | 0.043 | 0.000 | 0.091 | |
intercell_categories | 0.074 | 0.004 | 0.202 | |
intercell_consensus_filter | 2.121 | 0.159 | 5.512 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.079 | 0.005 | 0.189 | |
is_trembl | 0.081 | 0.000 | 0.210 | |
is_uniprot | 0.030 | 0.004 | 0.081 | |
kegg_info | 0.032 | 0.016 | 0.101 | |
kegg_open | 0.033 | 0.000 | 0.073 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.100 | 0.008 | 0.297 | |
kegg_pathway_list | 0.021 | 0.009 | 0.069 | |
kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
kegg_picture | 0.305 | 0.022 | 4.724 | |
kegg_process | 0.051 | 0.000 | 0.050 | |
latin_name | 0.153 | 0.004 | 0.172 | |
load_db | 0.186 | 0.016 | 0.262 | |
ncbi_taxid | 0.161 | 0.000 | 0.162 | |
nichenet_build_model | 0.000 | 0.000 | 0.001 | |
nichenet_expression_data | 0.033 | 0.000 | 0.032 | |
nichenet_gr_network | 0.082 | 0.004 | 0.088 | |
nichenet_gr_network_evex | 0.093 | 0.000 | 0.092 | |
nichenet_gr_network_harmonizome | 0.026 | 0.004 | 0.029 | |
nichenet_gr_network_htridb | 0.027 | 0.000 | 0.027 | |
nichenet_gr_network_omnipath | 17.306 | 0.534 | 21.776 | |
nichenet_gr_network_pathwaycommons | 0.017 | 0.008 | 0.025 | |
nichenet_gr_network_regnetwork | 0.053 | 0.033 | 0.133 | |
nichenet_gr_network_remap | 0.014 | 0.004 | 0.034 | |
nichenet_gr_network_trrust | 0.014 | 0.004 | 0.050 | |
nichenet_ligand_activities | 0.001 | 0.000 | 0.001 | |
nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.048 | 0.009 | 0.105 | |
nichenet_lr_network_guide2pharma | 0.019 | 0.000 | 0.018 | |
nichenet_lr_network_omnipath | 0.047 | 0.004 | 0.068 | |
nichenet_lr_network_ramilowski | 0.010 | 0.008 | 0.018 | |
nichenet_main | 0.001 | 0.000 | 0.001 | |
nichenet_networks | 0.108 | 0.008 | 0.117 | |
nichenet_optimization | 0.000 | 0.001 | 0.001 | |
nichenet_remove_orphan_ligands | 0.080 | 0.011 | 0.091 | |
nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
nichenet_signaling_network | 0.039 | 0.008 | 0.047 | |
nichenet_signaling_network_cpdb | 0.016 | 0.000 | 0.015 | |
nichenet_signaling_network_evex | 0.011 | 0.004 | 0.016 | |
nichenet_signaling_network_harmonizome | 0.011 | 0.005 | 0.015 | |
nichenet_signaling_network_inbiomap | 0.001 | 0.000 | 0.001 | |
nichenet_signaling_network_omnipath | 10.390 | 0.803 | 26.226 | |
nichenet_signaling_network_pathwaycommons | 0.011 | 0.000 | 0.011 | |
nichenet_signaling_network_vinayagam | 0.010 | 0.000 | 0.009 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.169 | 1.264 | 19.885 | |
omnipath | 4.675 | 0.384 | 6.187 | |
omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
omnipath_cache_clean | 0.013 | 0.000 | 0.038 | |
omnipath_cache_clean_db | 0.059 | 0.012 | 0.071 | |
omnipath_cache_download_ready | 0.651 | 3.002 | 6.299 | |
omnipath_cache_filter_versions | 0.139 | 0.012 | 0.178 | |
omnipath_cache_get | 0.146 | 0.000 | 0.146 | |
omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
omnipath_cache_latest_or_new | 0.073 | 0.004 | 0.076 | |
omnipath_cache_load | 0.704 | 1.787 | 12.748 | |
omnipath_cache_move_in | 0.181 | 0.048 | 0.257 | |
omnipath_cache_remove | 0.106 | 0.003 | 0.113 | |
omnipath_cache_save | 0.319 | 0.012 | 0.557 | |
omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
omnipath_cache_set_ext | 0.115 | 0.009 | 0.127 | |
omnipath_cache_update_status | 0.122 | 0.016 | 0.139 | |
omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
omnipath_get_config_path | 0.001 | 0.000 | 0.002 | |
omnipath_load_config | 0.000 | 0.000 | 0.001 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.000 | 0.002 | 0.004 | |
omnipath_msg | 0.006 | 0.005 | 0.010 | |
omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
omnipath_save_config | 0.000 | 0.000 | 0.001 | |
omnipath_set_cachedir | 0.060 | 0.032 | 0.093 | |
omnipath_set_console_loglevel | 0.000 | 0.001 | 0.001 | |
omnipath_set_logfile_loglevel | 0.000 | 0.001 | 0.001 | |
omnipath_set_loglevel | 0 | 0 | 0 | |
omnipath_show_db | 0.082 | 0.000 | 0.083 | |
omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
ontology_name_id | 0.001 | 0.000 | 0.001 | |
pathwaycommons_download | 0 | 0 | 0 | |
pivot_annotations | 17.280 | 1.644 | 42.469 | |
preppi_download | 0.001 | 0.001 | 0.001 | |
preppi_filter | 0.000 | 0.002 | 0.002 | |
print_bma_motif_es | 0.600 | 0.023 | 2.694 | |
print_bma_motif_vs | 0.351 | 0.032 | 1.925 | |
print_interactions | 9.932 | 0.462 | 19.328 | |
print_path_es | 1.021 | 0.049 | 3.024 | |
print_path_vs | 4.459 | 0.340 | 11.195 | |
pubmed_open | 8.698 | 0.561 | 18.925 | |
query_info | 0.212 | 0.011 | 0.816 | |
ramilowski_download | 0.002 | 0.000 | 0.007 | |
regnetwork_directions | 0.001 | 0.000 | 0.001 | |
regnetwork_download | 0.002 | 0.000 | 0.002 | |
relations_list_to_table | 0.220 | 0.004 | 0.465 | |
relations_table_to_graph | 0.001 | 0.000 | 0.000 | |
relations_table_to_list | 0.168 | 0.007 | 0.331 | |
remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
remap_filtered | 0.001 | 0.000 | 0.000 | |
remap_tf_target_download | 0.001 | 0.000 | 0.001 | |
resource_info | 0.334 | 0.065 | 1.685 | |
resources_colname | 0.986 | 0.077 | 3.635 | |
simplify_intercell_network | 0.002 | 0.000 | 0.006 | |
swap_relations | 0.274 | 0.024 | 0.754 | |
swissprots_only | 0.073 | 0.004 | 0.221 | |
tfcensus_download | 0.385 | 0.038 | 2.332 | |
translate_ids | 0.003 | 0.000 | 0.034 | |
trembls_only | 0.084 | 0.020 | 0.420 | |
trrust_download | 0.000 | 0.001 | 0.002 | |
uniprot_full_id_mapping_table | 0.002 | 0.000 | 0.026 | |
uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
uniprot_id_mapping_table | 0.001 | 0.000 | 0.009 | |
uniprot_id_type | 0.006 | 0.008 | 0.038 | |
unique_intercell_network | 0.001 | 0.000 | 0.001 | |
uploadlists_id_type | 0.018 | 0.000 | 0.099 | |
vinayagam_download | 0.002 | 0.000 | 0.010 | |
walk_ontology_tree | 0.003 | 0.000 | 0.027 | |
with_extra_attrs | 24.587 | 0.499 | 41.532 | |
with_references | 0.864 | 0.031 | 3.958 | |
zenodo_download | 0.000 | 0.002 | 0.018 | |