Denes Turei
| Snapshot Date: 2025-03-13 13:00 -0400 (Thu, 13 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-17 12:11 -0400 (Mon, 17 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4399 |
| 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 | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: /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_3.14.0.tar.gz |
| StartedAt: 2025-03-15 02:51:33 -0400 (Sat, 15 Mar 2025) |
| EndedAt: 2025-03-15 03:01:41 -0400 (Sat, 15 Mar 2025) |
| EllapsedTime: 608.4 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_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 13.7.1
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 02:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:57] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 02:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-15 02:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-15 02:51:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-15 02:51:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-15 02:51:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:51:58] [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
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 02:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 02:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-15 02:52:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-15 02:52:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-15 02:52:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-15 02:52:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 02:52:14] [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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: omnipath_for_cosmos
> ### Title: OmniPath PPI for the COSMOS PKN
> ### Aliases: omnipath_for_cosmos
>
> ### ** Examples
>
> op_cosmos <- omnipath_for_cosmos()
[2025-03-15 03:00:06] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Orthology targets:
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-15 03:00:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:07] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2025-03-15 03:00:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-15 03:00:07] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2025-03-15 03:00:07] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2025-03-15 03:00:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:07] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2025-03-15 03:00:11] [SUCCESS] [OmnipathR] Downloaded 81529 interactions.
[2025-03-15 03:00:11] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2025-03-15 03:00:11] [TRACE] [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
<Dataset name="hsapiens_gene_ensembl" interface="default" >
<Attribute name="uniprotswissprot"/>
<Attribute name="external_gene_name"/>
</Dataset>
</Query>
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-03-15 03:00:11] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:11] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-15 03:00:11] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-15 03:00:11] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-03-15 03:00:11] [TRACE] [OmnipathR] HTTP 200
[2025-03-15 03:00:12] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2025-03-15 03:00:12] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2025-03-15 03:00:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:12] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2025-03-15 03:00:12] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-15 03:00:12] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_113: DBI connect('database=ensembl_mart_113;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_113/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2025-03-15 03:00:12] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
▆
1. ├─OmnipathR::omnipath_for_cosmos()
2. │ └─... %T>% ...
3. ├─dplyr::bind_rows(...)
4. │ └─rlang::list2(...)
5. ├─OmnipathR::translate_ids_multi(...)
6. │ └─source_cols %>% seq_along %>% ...
7. ├─purrr::reduce(...)
8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
9. │ └─OmnipathR (local) fn(out, elt, ...)
10. │ └─OmnipathR::translate_ids(...)
11. │ └─d %<>% ...
12. ├─purrr::reduce2(...)
13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
15. │ ├─... %>% ...
16. │ └─OmnipathR:::id_translation_table(...)
17. │ └─OmnipathR::ensembl_id_mapping_table(...)
18. │ └─... %>% trim_and_distinct
19. ├─OmnipathR:::trim_and_distinct(.)
20. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
21. ├─dplyr::distinct(.)
22. ├─dplyr::mutate(., across(everything(), str_trim))
23. ├─rlang::set_names(., c("From", "To"))
24. └─rlang::abort(message = message)
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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/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 [2025-03-13 16:55:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 16:55:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 16:55:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:25] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 16:55:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 16:55:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 16:55:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:28] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2025-03-13 16:55:28] [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). [2025-03-13 16:55:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:28] [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). [2025-03-13 16:55:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:28] [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). [2025-03-13 16:55:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:28] [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). [2025-03-13 16:55:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 16:55:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 16:55:31] [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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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)
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:16] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Contains 3 files.
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-15 03:00:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-15 03:00:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-15 03:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-15 03:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-15 03:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-15 03:00:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-15 03:00:17] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
10.412 0.843 67.027
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.000 | |
| all_uniprot_acs | 0.014 | 0.002 | 0.016 | |
| all_uniprots | 0.772 | 0.095 | 90.478 | |
| ancestors | 0.008 | 0.001 | 0.009 | |
| annotated_network | 0.695 | 0.058 | 1.321 | |
| annotation_categories | 105.640 | 0.223 | 106.171 | |
| annotation_resources | 0.061 | 0.005 | 0.138 | |
| annotations | 0.230 | 0.019 | 0.331 | |
| biomart_query | 1.034 | 0.071 | 2.861 | |
| bioplex1 | 0.008 | 0.001 | 0.009 | |
| bioplex2 | 0.006 | 0.000 | 0.007 | |
| bioplex3 | 0.006 | 0.000 | 0.007 | |
| bioplex_all | 0.006 | 0.000 | 0.007 | |
| bioplex_hct116_1 | 0.007 | 0.000 | 0.008 | |
| bma_motif_es | 0.332 | 0.027 | 0.435 | |
| bma_motif_vs | 0.175 | 0.007 | 0.234 | |
| chalmers_gem | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_raw | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_reactions | 0.007 | 0.001 | 0.009 | |
| common_name | 0.033 | 0.000 | 0.033 | |
| complex_genes | 0.483 | 0.025 | 0.618 | |
| complex_resources | 0.057 | 0.003 | 0.107 | |
| complexes | 0.179 | 0.009 | 0.426 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.008 | 0.000 | 0.008 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 4.357 | 0.206 | 5.452 | |
| curated_ligrec_stats | 27.539 | 1.062 | 37.787 | |
| database_summary | 1.105 | 0.034 | 1.215 | |
| descendants | 0.007 | 0.000 | 0.008 | |
| ensembl_dataset | 0.01 | 0.00 | 0.01 | |
| ensembl_id_mapping_table | 1.353 | 0.074 | 32.171 | |
| ensembl_id_type | 0.002 | 0.001 | 0.002 | |
| ensembl_name | 0.103 | 0.002 | 0.106 | |
| ensembl_organisms | 0.111 | 0.003 | 0.114 | |
| ensembl_organisms_raw | 0.133 | 0.004 | 0.136 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 2.361 | 0.064 | 2.537 | |
| enzsub_resources | 0.056 | 0.003 | 0.107 | |
| enzyme_substrate | 0.953 | 0.012 | 1.013 | |
| evex_download | 0.007 | 0.001 | 0.008 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 9.750 | 0.158 | 10.032 | |
| extra_attrs | 6.210 | 0.034 | 6.251 | |
| extra_attrs_to_cols | 8.829 | 0.051 | 9.106 | |
| filter_by_resource | 4.394 | 0.090 | 4.655 | |
| filter_extra_attrs | 17.145 | 0.075 | 17.294 | |
| filter_intercell | 6.096 | 0.350 | 6.664 | |
| filter_intercell_network | 0.016 | 0.001 | 0.017 | |
| find_all_paths | 5.316 | 0.104 | 5.425 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.011 | 0.001 | 0.012 | |
| giant_component | 9.001 | 0.285 | 9.349 | |
| go_annot_download | 13.011 | 0.571 | 13.138 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.007 | 0.000 | 0.009 | |
| guide2pharma_download | 0.007 | 0.001 | 0.008 | |
| harmonizome_download | 0.007 | 0.001 | 0.008 | |
| has_extra_attrs | 6.049 | 0.067 | 6.122 | |
| hmdb_id_mapping_table | 0.007 | 0.001 | 0.008 | |
| hmdb_id_type | 0.002 | 0.001 | 0.002 | |
| hmdb_metabolite_fields | 0.001 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_table | 0.008 | 0.001 | 0.008 | |
| homologene_download | 0.007 | 0.001 | 0.008 | |
| homologene_raw | 0.018 | 0.001 | 0.019 | |
| homologene_uniprot_orthology | 0.009 | 0.001 | 0.010 | |
| hpo_download | 1.548 | 0.124 | 2.915 | |
| htridb_download | 0.007 | 0.001 | 0.008 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.033 | 0.000 | 0.034 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0.000 | 0.001 | 0.001 | |
| interaction_datasets | 0.285 | 0.021 | 0.339 | |
| interaction_graph | 0.374 | 0.012 | 0.435 | |
| interaction_resources | 0.046 | 0.005 | 0.097 | |
| interaction_types | 0.036 | 0.002 | 0.038 | |
| intercell | 0.358 | 0.029 | 0.428 | |
| intercell_categories | 0.290 | 0.031 | 0.352 | |
| intercell_consensus_filter | 0.622 | 0.068 | 0.719 | |
| intercell_generic_categories | 0.024 | 0.002 | 0.027 | |
| intercell_network | 0.003 | 0.000 | 0.004 | |
| intercell_resources | 0.025 | 0.003 | 0.259 | |
| intercell_summary | 0.036 | 0.012 | 0.048 | |
| is_ontology_id | 0.001 | 0.000 | 0.001 | |
| is_swissprot | 0.019 | 0.001 | 0.020 | |
| is_trembl | 0.013 | 0.001 | 0.014 | |
| is_uniprot | 0.005 | 0.001 | 0.006 | |
| kegg_info | 0.007 | 0.001 | 0.008 | |
| kegg_open | 0.046 | 0.005 | 0.052 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.006 | 0.001 | 0.007 | |
| kegg_pathway_list | 0.006 | 0.001 | 0.007 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 0.058 | 0.010 | 2.701 | |
| kegg_process | 0.014 | 0.001 | 0.016 | |
| latin_name | 0.057 | 0.000 | 0.058 | |
| load_db | 0.057 | 0.002 | 0.059 | |
| ncbi_taxid | 0.053 | 0.001 | 0.054 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.007 | 0.000 | 0.008 | |
| nichenet_gr_network | 0.019 | 0.002 | 0.021 | |
| nichenet_gr_network_evex | 0.007 | 0.000 | 0.007 | |
| nichenet_gr_network_harmonizome | 0.007 | 0.000 | 0.007 | |
| nichenet_gr_network_htridb | 0.007 | 0.001 | 0.007 | |
| nichenet_gr_network_omnipath | 11.179 | 0.696 | 12.087 | |
| nichenet_gr_network_pathwaycommons | 0.055 | 0.006 | 0.061 | |
| nichenet_gr_network_regnetwork | 0.006 | 0.001 | 0.007 | |
| nichenet_gr_network_remap | 0.006 | 0.001 | 0.007 | |
| nichenet_gr_network_trrust | 0.007 | 0.001 | 0.007 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.000 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.021 | 0.002 | 0.024 | |
| nichenet_lr_network_guide2pharma | 0.007 | 0.001 | 0.008 | |
| nichenet_lr_network_omnipath | 0.022 | 0.003 | 0.025 | |
| nichenet_lr_network_ramilowski | 0.006 | 0.001 | 0.007 | |
| nichenet_main | 0.000 | 0.001 | 0.001 | |
| nichenet_networks | 0.032 | 0.004 | 0.036 | |
| nichenet_optimization | 0.000 | 0.000 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.018 | 0.001 | 0.020 | |
| nichenet_results_dir | 0.001 | 0.001 | 0.000 | |
| nichenet_signaling_network | 0.019 | 0.002 | 0.021 | |
| nichenet_signaling_network_cpdb | 0.006 | 0.001 | 0.007 | |
| nichenet_signaling_network_evex | 0.006 | 0.000 | 0.007 | |
| nichenet_signaling_network_harmonizome | 0.006 | 0.000 | 0.007 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 9.298 | 0.471 | 12.607 | |
| nichenet_signaling_network_pathwaycommons | 0.008 | 0.001 | 0.009 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.001 | 0.008 | |
| nichenet_test | 0.000 | 0.001 | 0.000 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.082 | 0.007 | 0.509 | |
| oma_code | 0.029 | 0.000 | 0.030 | |
| oma_organisms | 0.050 | 0.001 | 0.052 | |
| oma_pairwise | 0.008 | 0.001 | 0.009 | |
| oma_pairwise_genesymbols | 0.065 | 0.001 | 0.066 | |
| oma_pairwise_translated | 0.010 | 0.000 | 0.011 | |
| omnipath-interactions | 25.914 | 0.731 | 28.860 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.005 | 0.001 | 0.006 | |
| omnipath_cache_clean_db | 0.153 | 0.006 | 0.160 | |
| omnipath_cache_download_ready | 0.473 | 0.032 | 0.686 | |
| omnipath_cache_filter_versions | 0.058 | 0.009 | 0.075 | |
| omnipath_cache_get | 0.100 | 0.009 | 0.109 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.058 | 0.006 | 0.064 | |
| omnipath_cache_load | 0.361 | 0.024 | 0.743 | |
| omnipath_cache_move_in | 0.128 | 0.018 | 0.150 | |
| omnipath_cache_remove | 0.149 | 0.014 | 0.167 | |
| omnipath_cache_save | 0.147 | 0.015 | 0.177 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.066 | 0.009 | 0.078 | |
| omnipath_cache_update_status | 0.074 | 0.011 | 0.084 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |