Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:39 -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: 2023-04-12 08:00:25 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 08:28:50 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 1705.1 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 Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 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 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 [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Contains 1 files. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-12 08:00:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:00:55] [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 77.983 0.039 79.521 curated_ligrec_stats 39.454 1.201 112.729 filter_extra_attrs 38.637 0.195 40.034 has_extra_attrs 10.294 25.066 183.932 with_extra_attrs 21.843 0.157 33.965 giant_component 20.007 0.176 45.807 go_annot_download 16.019 4.042 71.163 extra_attr_values 17.487 0.420 20.293 nichenet_gr_network_omnipath 16.685 0.196 21.095 pivot_annotations 15.883 0.414 31.758 extra_attrs_to_cols 15.193 0.172 15.366 find_all_paths 12.865 0.111 27.223 extra_attrs 10.858 0.160 11.039 get_signed_ptms 10.581 0.012 19.871 nichenet_signaling_network_omnipath 10.443 0.137 13.060 filter_intercell 9.601 0.328 23.244 pubmed_open 9.221 0.172 12.087 filter_by_resource 8.301 0.142 10.706 print_interactions 7.187 0.179 11.201 curated_ligand_receptor_interactions 6.476 0.229 16.600 collectri 4.607 0.120 6.447 print_path_vs 3.442 0.134 7.048 import_transcriptional_interactions 2.824 0.061 7.126 enzsub_graph 2.558 0.108 5.104 intercell_consensus_filter 2.380 0.088 7.081 dorothea 2.202 0.104 5.001 biomart_query 1.742 0.056 9.511 ensembl_id_mapping_table 1.248 0.040 21.631 kegg_picture 0.135 0.023 5.593 * 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: 1 NOTE 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 [2023-04-12 01:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Contains 6 files. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 01:51:20] [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). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [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). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [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). [2023-04-12 01:51:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:20] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Contains 1 files. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-12 01:51:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 01:51:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 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) [2023-04-12 08:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 08:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:48] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Contains 15 files. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 08:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 08:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-12 08:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-12 08:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 08:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-12 08:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 08:17:49] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 16.879 1.365 60.058
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.036 | 0.000 | 0.035 | |
all_uniprots | 0.014 | 0.000 | 0.014 | |
ancestors | 0.012 | 0.000 | 0.012 | |
annotated_network | 1.347 | 0.065 | 4.523 | |
annotation_categories | 77.983 | 0.039 | 79.521 | |
biomart_query | 1.742 | 0.056 | 9.511 | |
bioplex1 | 0.013 | 0.000 | 0.013 | |
bioplex2 | 0.012 | 0.000 | 0.013 | |
bioplex3 | 0.012 | 0.000 | 0.012 | |
bioplex_all | 0.012 | 0.000 | 0.012 | |
bioplex_hct116_1 | 0.008 | 0.004 | 0.013 | |
bma_motif_es | 0.459 | 0.020 | 1.357 | |
bma_motif_vs | 0.153 | 0.000 | 0.946 | |
collectri | 4.607 | 0.120 | 6.447 | |
common_name | 0.056 | 0.000 | 0.057 | |
consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
consensuspathdb_raw_table | 0.011 | 0.000 | 0.011 | |
curated_ligand_receptor_interactions | 6.476 | 0.229 | 16.600 | |
curated_ligrec_stats | 39.454 | 1.201 | 112.729 | |
database_summary | 1.853 | 0.326 | 4.785 | |
descendants | 0.013 | 0.000 | 0.014 | |
dorothea | 2.202 | 0.104 | 5.001 | |
ensembl_dataset | 0.014 | 0.000 | 0.014 | |
ensembl_id_mapping_table | 1.248 | 0.040 | 21.631 | |
ensembl_id_type | 0.009 | 0.000 | 0.009 | |
ensembl_name | 0.101 | 0.004 | 0.104 | |
ensembl_organisms | 0.414 | 0.004 | 0.420 | |
ensembl_organisms_raw | 0.326 | 0.000 | 0.328 | |
ensembl_orthology | 0.000 | 0.000 | 0.001 | |
enzsub_graph | 2.558 | 0.108 | 5.104 | |
evex_download | 0.012 | 0.000 | 0.013 | |
extra_attr_values | 17.487 | 0.420 | 20.293 | |
extra_attrs | 10.858 | 0.160 | 11.039 | |
extra_attrs_to_cols | 15.193 | 0.172 | 15.366 | |
filter_by_resource | 8.301 | 0.142 | 10.706 | |
filter_extra_attrs | 38.637 | 0.195 | 40.034 | |
filter_intercell | 9.601 | 0.328 | 23.244 | |
filter_intercell_network | 0.052 | 0.000 | 0.140 | |
find_all_paths | 12.865 | 0.111 | 27.223 | |
get_annotation_resources | 0.114 | 0.012 | 1.073 | |
get_complex_genes | 1.497 | 0.060 | 4.166 | |
get_complex_resources | 0.101 | 0.000 | 1.000 | |
get_db | 0.000 | 0.000 | 0.001 | |
get_enzsub_resources | 0.132 | 0.000 | 0.842 | |
get_interaction_resources | 0.170 | 0.004 | 1.041 | |
get_intercell_categories | 0.421 | 0.008 | 1.002 | |
get_intercell_generic_categories | 0.041 | 0.000 | 0.041 | |
get_intercell_resources | 0.170 | 0.000 | 1.014 | |
get_ontology_db | 0.020 | 0.004 | 0.068 | |
get_resources | 0.099 | 0.016 | 0.833 | |
get_signed_ptms | 10.581 | 0.012 | 19.871 | |
giant_component | 20.007 | 0.176 | 45.807 | |
go_annot_download | 16.019 | 4.042 | 71.163 | |
go_annot_slim | 0.005 | 0.004 | 1.128 | |
go_ontology_download | 0.018 | 0.000 | 0.027 | |
guide2pharma_download | 0.014 | 0.000 | 0.035 | |
harmonizome_download | 0.008 | 0.000 | 0.008 | |
has_extra_attrs | 10.294 | 25.066 | 183.932 | |
homologene_download | 0.013 | 0.000 | 0.018 | |
homologene_raw | 0.016 | 0.012 | 0.079 | |
homologene_uniprot_orthology | 0.007 | 0.004 | 0.010 | |
homology_translate | 0.001 | 0.000 | 0.000 | |
hpo_download | 1.244 | 0.111 | 2.403 | |
htridb_download | 0.013 | 0.000 | 0.012 | |
import_all_interactions | 1.427 | 0.136 | 4.470 | |
import_intercell_network | 0.006 | 0.004 | 0.010 | |
import_kinaseextra_interactions | 1.048 | 0.071 | 3.391 | |
import_ligrecextra_interactions | 0.587 | 0.075 | 2.282 | |
import_lncrna_mrna_interactions | 0.475 | 0.021 | 1.517 | |
import_mirnatarget_interactions | 0.805 | 0.062 | 2.643 | |
import_omnipath_annotations | 0.350 | 0.033 | 1.422 | |
import_omnipath_complexes | 0.444 | 0.015 | 2.227 | |
import_omnipath_enzsub | 0.982 | 0.007 | 1.625 | |
import_omnipath_interactions | 0.265 | 0.004 | 1.271 | |
import_omnipath_intercell | 0.362 | 0.040 | 0.956 | |
import_pathwayextra_interactions | 1.089 | 0.118 | 4.142 | |
import_post_translational_interactions | 1.229 | 0.035 | 3.857 | |
import_small_molecule_protein_interactions | 0.548 | 0.011 | 1.147 | |
import_tf_mirna_interactions | 0.984 | 0.046 | 2.901 | |
import_tf_target_interactions | 1.059 | 0.036 | 2.906 | |
import_transcriptional_interactions | 2.824 | 0.061 | 7.126 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.606 | 0.020 | 1.845 | |
interaction_graph | 0.521 | 0.009 | 1.985 | |
interaction_types | 0.033 | 0.004 | 0.069 | |
intercell_categories | 0.142 | 0.000 | 0.284 | |
intercell_consensus_filter | 2.380 | 0.088 | 7.081 | |
is_ontology_id | 0.001 | 0.000 | 0.000 | |
is_swissprot | 0.060 | 0.000 | 0.119 | |
is_trembl | 0.056 | 0.000 | 0.104 | |
is_uniprot | 0.020 | 0.000 | 0.035 | |
kegg_info | 0.020 | 0.012 | 0.064 | |
kegg_open | 0.019 | 0.003 | 0.038 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.015 | 0.007 | 0.038 | |
kegg_pathway_list | 0.016 | 0.008 | 0.056 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.135 | 0.023 | 5.593 | |
kegg_process | 0.048 | 0.000 | 0.120 | |
latin_name | 0.136 | 0.003 | 0.348 | |
load_db | 0.173 | 0.005 | 0.365 | |
ncbi_taxid | 0.125 | 0.000 | 0.236 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.026 | 0.001 | 0.059 | |
nichenet_gr_network | 0.077 | 0.016 | 0.189 | |
nichenet_gr_network_evex | 0.016 | 0.003 | 0.035 | |
nichenet_gr_network_harmonizome | 0.012 | 0.008 | 0.035 | |
nichenet_gr_network_htridb | 0.019 | 0.000 | 0.035 | |
nichenet_gr_network_omnipath | 16.685 | 0.196 | 21.095 | |
nichenet_gr_network_pathwaycommons | 0.021 | 0.000 | 0.020 | |
nichenet_gr_network_regnetwork | 0.020 | 0.000 | 0.019 | |
nichenet_gr_network_remap | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_trrust | 0.019 | 0.000 | 0.019 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.068 | 0.000 | 0.068 | |
nichenet_lr_network_guide2pharma | 0.020 | 0.004 | 0.024 | |
nichenet_lr_network_omnipath | 0.061 | 0.003 | 0.065 | |
nichenet_lr_network_ramilowski | 0.023 | 0.000 | 0.022 | |
nichenet_main | 0.000 | 0.000 | 0.001 | |
nichenet_networks | 0.083 | 0.024 | 0.107 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.054 | 0.004 | 0.059 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.06 | 0.00 | 0.06 | |
nichenet_signaling_network_cpdb | 0.02 | 0.00 | 0.02 | |
nichenet_signaling_network_evex | 0.082 | 0.004 | 0.085 | |
nichenet_signaling_network_harmonizome | 0.022 | 0.000 | 0.022 | |
nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
nichenet_signaling_network_omnipath | 10.443 | 0.137 | 13.060 | |
nichenet_signaling_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
nichenet_signaling_network_vinayagam | 0.009 | 0.000 | 0.009 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.094 | 0.000 | 0.131 | |
omnipath | 3.258 | 0.001 | 3.259 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.013 | 0.000 | 0.013 | |
omnipath_cache_clean_db | 0.100 | 0.008 | 0.108 | |
omnipath_cache_download_ready | 0.399 | 0.020 | 0.439 | |
omnipath_cache_filter_versions | 0.229 | 0.004 | 0.257 | |
omnipath_cache_get | 0.131 | 0.008 | 0.139 | |
omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
omnipath_cache_latest_or_new | 0.095 | 0.008 | 0.102 | |
omnipath_cache_load | 0.847 | 0.023 | 3.786 | |
omnipath_cache_move_in | 0.401 | 0.025 | 0.705 | |
omnipath_cache_remove | 0.291 | 0.003 | 0.332 | |
omnipath_cache_save | 0.334 | 0.009 | 0.502 | |
omnipath_cache_search | 0.000 | 0.001 | 0.005 | |
omnipath_cache_set_ext | 0.145 | 0.004 | 0.228 | |
omnipath_cache_update_status | 0.169 | 0.000 | 0.272 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_get_config_path | 0.001 | 0.000 | 0.001 | |
omnipath_load_config | 0.000 | 0.000 | 0.001 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.001 | 0.000 | 0.001 | |
omnipath_msg | 0.010 | 0.000 | 0.024 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.046 | 0.003 | 0.085 | |
omnipath_set_console_loglevel | 0.002 | 0.000 | 0.002 | |
omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
omnipath_set_loglevel | 0.000 | 0.002 | 0.013 | |
omnipath_show_db | 0.151 | 0.001 | 0.288 | |
omnipath_unlock_cache_db | 0 | 0 | 0 | |
ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
ontology_name_id | 0.000 | 0.000 | 0.001 | |
pathwaycommons_download | 0 | 0 | 0 | |
pivot_annotations | 15.883 | 0.414 | 31.758 | |
preppi_download | 0.000 | 0.000 | 0.001 | |
preppi_filter | 0.001 | 0.000 | 0.001 | |
print_bma_motif_es | 0.238 | 0.017 | 1.293 | |
print_bma_motif_vs | 0.155 | 0.000 | 0.950 | |
print_interactions | 7.187 | 0.179 | 11.201 | |
print_path_es | 0.732 | 0.017 | 3.249 | |
print_path_vs | 3.442 | 0.134 | 7.048 | |
pubmed_open | 9.221 | 0.172 | 12.087 | |
query_info | 0.099 | 0.004 | 0.468 | |
ramilowski_download | 0.000 | 0.000 | 0.001 | |
regnetwork_directions | 0.001 | 0.000 | 0.001 | |
regnetwork_download | 0.001 | 0.000 | 0.000 | |
relations_list_to_table | 0.172 | 0.001 | 0.206 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.15 | 0.00 | 0.20 | |
remap_dorothea_download | 0.000 | 0.000 | 0.001 | |
remap_filtered | 0.001 | 0.000 | 0.000 | |
remap_tf_target_download | 0.001 | 0.000 | 0.000 | |
resource_info | 0.192 | 0.012 | 0.899 | |
resources_colname | 0.764 | 0.034 | 2.826 | |
simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
swap_relations | 0.208 | 0.008 | 0.284 | |
swissprots_only | 0.055 | 0.000 | 0.055 | |
tfcensus_download | 0.224 | 0.004 | 0.557 | |
translate_ids | 0.001 | 0.000 | 0.001 | |
trembls_only | 0.06 | 0.00 | 0.10 | |
trrust_download | 0.000 | 0.001 | 0.001 | |
uniprot_full_id_mapping_table | 0.000 | 0.001 | 0.001 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0.001 | 0.000 | 0.017 | |
uniprot_id_type | 0.008 | 0.000 | 0.009 | |
unique_intercell_network | 0.001 | 0.000 | 0.001 | |
uploadlists_id_type | 0.008 | 0.000 | 0.008 | |
vinayagam_download | 0.001 | 0.000 | 0.001 | |
walk_ontology_tree | 0.001 | 0.000 | 0.006 | |
with_extra_attrs | 21.843 | 0.157 | 33.965 | |
with_references | 0.708 | 0.013 | 3.225 | |
zenodo_download | 0.001 | 0.000 | 0.001 | |