Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:40 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 1467/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.12.0 (landing page) Denes Turei
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | ||||||||
To the developers/maintainers of the OmnipathR package: - 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: 3.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.0.tar.gz |
StartedAt: 2024-05-06 23:31:15 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 23:37:35 -0400 (Mon, 06 May 2024) |
EllapsedTime: 380.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/OmnipathR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.12.0’ * 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 ... NOTE License stub is invalid DCF. * 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 [2024-05-06 23:31:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:31:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 23:31:24] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:24] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 23:31:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 23:31:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:31:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:25] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 23:31:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 23:31:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 23:31:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 23:31:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 23:31:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:25] [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 [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 23:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:31:29] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘oma_pairwise_translated’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: organism_for > ### Title: Make sure the resource supports the organism and it has the ID > ### Aliases: organism_for > > ### ** Examples > > organism_for(10116, 'chalmers-gem') [1] "Rat" > # [1] "Rat" > organism_for(6239, 'chalmers-gem') Error in organism_for(6239, "chalmers-gem") : Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758). Execution halted * 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: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/OmnipathR.Rcheck/00check.log’ for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 [2024-05-06 15:39:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:39:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:57] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:39:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 15:39:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 15:39:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 15:39:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 15:39:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:39:58] [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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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) [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 23:36:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 23:36:53] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 3.537 0.345 37.131
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.006 | 0.001 | 0.007 | |
all_uniprots | 0.003 | 0.001 | 0.003 | |
ancestors | 0.002 | 0.000 | 0.003 | |
annotated_network | 0.504 | 0.046 | 6.407 | |
annotation_categories | 35.090 | 0.024 | 36.570 | |
biomart_query | 0.275 | 0.025 | 3.908 | |
bioplex1 | 0.004 | 0.000 | 0.004 | |
bioplex2 | 0.003 | 0.001 | 0.004 | |
bioplex3 | 0.003 | 0.000 | 0.003 | |
bioplex_all | 0.003 | 0.001 | 0.004 | |
bioplex_hct116_1 | 0.003 | 0.000 | 0.003 | |
bma_motif_es | 0.092 | 0.012 | 0.987 | |
bma_motif_vs | 0.048 | 0.002 | 0.592 | |
collectri | 30.698 | 0.135 | 33.861 | |
common_name | 0.006 | 0.001 | 0.006 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.017 | 0.000 | 0.016 | |
curated_ligand_receptor_interactions | 1.238 | 0.092 | 11.037 | |
curated_ligrec_stats | 8.394 | 0.489 | 72.058 | |
database_summary | 0.418 | 0.015 | 2.880 | |
descendants | 0.004 | 0.001 | 0.004 | |
dorothea | 16.740 | 0.118 | 19.396 | |
ensembl_dataset | 0.002 | 0.000 | 0.003 | |
ensembl_id_mapping_table | 0.254 | 0.022 | 10.457 | |
ensembl_id_type | 0.001 | 0.000 | 0.001 | |
ensembl_name | 0.01 | 0.00 | 0.01 | |
ensembl_organisms | 0.032 | 0.001 | 0.033 | |
ensembl_organisms_raw | 0.030 | 0.001 | 0.031 | |
ensembl_orthology | 0.000 | 0.000 | 0.001 | |
enzsub_graph | 0.591 | 0.023 | 2.599 | |
evex_download | 0.003 | 0.000 | 0.004 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 4.322 | 0.066 | 8.199 | |
extra_attrs | 1.971 | 0.010 | 2.464 | |
extra_attrs_to_cols | 4.314 | 0.020 | 5.815 | |
filter_by_resource | 2.534 | 0.059 | 5.661 | |
filter_extra_attrs | 6.269 | 0.031 | 7.620 | |
filter_intercell | 2.331 | 0.161 | 7.224 | |
filter_intercell_network | 0.006 | 0.000 | 0.007 | |
find_all_paths | 1.560 | 0.042 | 1.602 | |
from_evidences | 0.000 | 0.000 | 0.001 | |
get_annotation_resources | 0.018 | 0.002 | 0.559 | |
get_complex_genes | 0.401 | 0.021 | 2.501 | |
get_complex_resources | 0.018 | 0.002 | 0.651 | |
get_db | 0 | 0 | 0 | |
get_enzsub_resources | 0.018 | 0.001 | 0.635 | |
get_interaction_resources | 0.031 | 0.002 | 0.575 | |
get_intercell_categories | 0.075 | 0.011 | 0.329 | |
get_intercell_generic_categories | 0.009 | 0.001 | 0.011 | |
get_intercell_resources | 0.017 | 0.001 | 0.649 | |
get_ontology_db | 0.003 | 0.001 | 0.004 | |
get_resources | 0.019 | 0.002 | 0.565 | |
get_signed_ptms | 1.663 | 0.053 | 2.263 | |
giant_component | 3.263 | 0.097 | 6.460 | |
go_annot_download | 3.432 | 0.170 | 3.815 | |
go_annot_slim | 0.000 | 0.000 | 0.001 | |
go_ontology_download | 0.003 | 0.000 | 0.003 | |
guide2pharma_download | 0.003 | 0.001 | 0.004 | |
harmonizome_download | 0.003 | 0.000 | 0.003 | |
has_extra_attrs | 1.851 | 0.028 | 1.878 | |
homologene_download | 0.003 | 0.000 | 0.003 | |
homologene_raw | 0.005 | 0.001 | 0.005 | |
homologene_uniprot_orthology | 0.003 | 0.000 | 0.003 | |
hpo_download | 0.845 | 0.068 | 2.269 | |
htridb_download | 0.003 | 0.000 | 0.003 | |
import_all_interactions | 0.665 | 0.037 | 3.415 | |
import_intercell_network | 0.003 | 0.000 | 0.004 | |
import_kinaseextra_interactions | 0.419 | 0.022 | 2.710 | |
import_ligrecextra_interactions | 0.187 | 0.015 | 1.740 | |
import_lncrna_mrna_interactions | 0.140 | 0.013 | 0.999 | |
import_mirnatarget_interactions | 0.254 | 0.016 | 1.881 | |
import_omnipath_annotations | 0.160 | 0.012 | 0.943 | |
import_omnipath_complexes | 0.163 | 0.015 | 1.872 | |
import_omnipath_enzsub | 0.331 | 0.004 | 0.878 | |
import_omnipath_interactions | 0.074 | 0.002 | 0.614 | |
import_omnipath_intercell | 0.125 | 0.012 | 0.682 | |
import_pathwayextra_interactions | 0.215 | 0.017 | 1.912 | |
import_post_translational_interactions | 0.231 | 0.018 | 1.950 | |
import_small_molecule_protein_interactions | 0.120 | 0.010 | 0.365 | |
import_tf_mirna_interactions | 0.198 | 0.017 | 1.369 | |
import_tf_target_interactions | 0.367 | 0.021 | 2.300 | |
import_transcriptional_interactions | 0.739 | 0.029 | 2.824 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.010 | 0.001 | 0.011 | |
interaction_graph | 0.112 | 0.003 | 0.731 | |
interaction_types | 0.030 | 0.001 | 0.030 | |
intercell_categories | 0.017 | 0.001 | 0.018 | |
intercell_consensus_filter | 0.446 | 0.035 | 2.057 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.009 | 0.001 | 0.010 | |
is_trembl | 0.008 | 0.000 | 0.008 | |
is_uniprot | 0.003 | 0.001 | 0.004 | |
kegg_info | 0.004 | 0.000 | 0.003 | |
kegg_open | 0.002 | 0.000 | 0.003 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.003 | 0.001 | 0.003 | |
kegg_pathway_list | 0.003 | 0.000 | 0.004 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.025 | 0.006 | 4.745 | |
kegg_process | 0.007 | 0.001 | 0.007 | |
latin_name | 0.013 | 0.000 | 0.013 | |
load_db | 0.023 | 0.001 | 0.023 | |
ncbi_taxid | 0.011 | 0.000 | 0.011 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.003 | 0.000 | 0.004 | |
nichenet_gr_network | 0.009 | 0.001 | 0.009 | |
nichenet_gr_network_evex | 0.003 | 0.000 | 0.003 | |
nichenet_gr_network_harmonizome | 0.003 | 0.001 | 0.004 | |
nichenet_gr_network_htridb | 0.019 | 0.000 | 0.020 | |
nichenet_gr_network_omnipath | 3.997 | 0.196 | 6.479 | |
nichenet_gr_network_pathwaycommons | 0.004 | 0.001 | 0.005 | |
nichenet_gr_network_regnetwork | 0.003 | 0.000 | 0.003 | |
nichenet_gr_network_remap | 0.003 | 0.000 | 0.004 | |
nichenet_gr_network_trrust | 0.002 | 0.001 | 0.003 | |
nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.009 | 0.000 | 0.009 | |
nichenet_lr_network_guide2pharma | 0.003 | 0.000 | 0.003 | |
nichenet_lr_network_omnipath | 0.008 | 0.001 | 0.009 | |
nichenet_lr_network_ramilowski | 0.003 | 0.000 | 0.003 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.028 | 0.001 | 0.030 | |
nichenet_optimization | 0.001 | 0.000 | 0.000 | |
nichenet_remove_orphan_ligands | 0.009 | 0.001 | 0.011 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.011 | 0.001 | 0.011 | |
nichenet_signaling_network_cpdb | 0.003 | 0.000 | 0.003 | |
nichenet_signaling_network_evex | 0.002 | 0.001 | 0.003 | |
nichenet_signaling_network_harmonizome | 0.002 | 0.000 | 0.003 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 3.134 | 0.171 | 5.755 | |
nichenet_signaling_network_pathwaycommons | 0.003 | 0.000 | 0.004 | |
nichenet_signaling_network_vinayagam | 0.002 | 0.000 | 0.003 | |
nichenet_test | 0.000 | 0.001 | 0.000 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.043 | 0.002 | 0.101 | |
oma_code | 0.006 | 0.001 | 0.006 | |
oma_organisms | 0.017 | 0.000 | 0.017 | |
oma_pairwise | 0.003 | 0.001 | 0.004 | |
oma_pairwise_genesymbols | 0.003 | 0.000 | 0.003 | |
omnipath | 1.173 | 0.014 | 1.186 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.002 | 0.000 | 0.002 | |
omnipath_cache_clean_db | 0.022 | 0.002 | 0.025 | |
omnipath_cache_download_ready | 0.119 | 0.013 | 0.199 | |
omnipath_cache_filter_versions | 0.025 | 0.004 | 0.064 | |
omnipath_cache_get | 0.030 | 0.003 | 0.034 | |
omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
omnipath_cache_latest_or_new | 0.015 | 0.003 | 0.017 | |
omnipath_cache_load | 0.182 | 0.011 | 2.650 | |
omnipath_cache_move_in | 0.039 | 0.005 | 0.055 | |
omnipath_cache_remove | 0.025 | 0.003 | 0.040 | |
omnipath_cache_save | 0.049 | 0.007 | 0.071 | |
omnipath_cache_search | 0 | 0 | 0 | |
omnipath_cache_set_ext | 0.021 | 0.003 | 0.035 | |
omnipath_cache_update_status | 0.022 | 0.002 | 0.024 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_get_config_path | 0 | 0 | 0 | |
omnipath_load_config | 0.000 | 0.001 | 0.000 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0.001 | 0.000 | 0.001 | |
omnipath_msg | 0.001 | 0.000 | 0.001 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.006 | 0.001 | 0.007 | |
omnipath_set_console_loglevel | 0 | 0 | 0 | |
omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.000 | |
omnipath_set_loglevel | 0 | 0 | 0 | |
omnipath_show_db | 0.012 | 0.000 | 0.012 | |
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 | 0.000 | 0.000 | 0.001 | |