[ Started: 2024-04-03 18:17:33 CEST ]
[ OmnipathR v3.10.1 for BioC-3.18 from https://github.com/saezlab/OmnipathR@RELEASE_3_18 (b1b2bab 2023-10-25 17:47:10) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.10.1’
* 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 executable files ... 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 ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-03 18:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:52] [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
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-03 18:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:17:59] [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2024-04-03 18:23:26] [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="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2024-04-03 18:23:26] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-04-03 18:23:26] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-04-03 18:23:26] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:23:26] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-04-03 18:23:26] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-04-03 18:23:26] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-04-03 18:23:26] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-03 18:23:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-03 18:23:26] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2024-04-03 18:23:26] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <html>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <head>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <style>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] html,
[2024-04-03 18:23:26] [WARN]    [OmnipathR] body {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] padding: 0;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] margin: 0;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] height: 100%;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] body {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] display: grid;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] font-size: 90%;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] h1 {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] font-size: 1.5rem;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] h2 {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] font-size: 1.2rem;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] h3 {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] font-size: 1.1rem;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] header {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] grid-row: header;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] padding: 5px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] height: 60px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] background-color: #333366;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] header img {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] width: 185px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] height: 45px
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] main {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] grid-row: main;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] padding: 20px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] .mirrors {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] margin-top: 20px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] padding: 10px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] footer {
[2024-04-03 18:23:26] [WARN]    [OmnipathR] grid-row: footer;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] padding: 0 20px;
[2024-04-03 18:23:26] [WARN]    [OmnipathR] }
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </style>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </head>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <body>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <header>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </header>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <main>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <p>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2024-04-03 18:23:26] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2024-04-03 18:23:26] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </p>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <div class="mirrors">
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <ul>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </ul>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2024-04-03 18:23:26] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2024-04-03 18:23:26] [WARN]    [OmnipathR] data centre.
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </div>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </main>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <footer>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </footer>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </body>
[2024-04-03 18:23:26] [WARN]    [OmnipathR] </html>
[2024-04-03 18:23:26] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
    ▆
 1. ├─OmnipathR::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─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 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 ERROR, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-04-03_1810/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-04-03 18:29:15 CEST ]