[ Started: 2025-03-16 00:39:54 CET ]
[ OmnipathR v3.14.0 for BioC-3.20 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_20 (3c7d7f1 2024-10-29 10:41:00) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* 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 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  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:19] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:19] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-16 00:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-16 00:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-16 00:40:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:20] [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
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-16 00:40:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:40:29] [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")
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-03-16 00:43:01] [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>
[2025-03-16 00:43:01] [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`.
[2025-03-16 00:43:01] [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`
[2025-03-16 00:43:01] [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`.
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:43:01] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-16 00:43:01] [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`
[2025-03-16 00:43:01] [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`
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] HTTP 200
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-16 00:43:01] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-16 00:43:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-16 00:43:01] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-03-16 00:43:01] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-16 00:43:01] [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.
[2025-03-16 00:43:01] [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::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 ... OK
* 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-3.20/2025-03-16_0032/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-03-16 00:49:55 CET ]