[ Started: 2024-10-10 16:04:23 CEST ]
[ OmnipathR v3.12.4 for BioC-3.19 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_19 (edb3c69 2024-10-02 12:46:04) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/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 ‘3.12.4’
* 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   4.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Licence 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-10 16:04:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:43] [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
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:04:49] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_organisms: no visible binding for global variable ‘ncbi_tax_id’
Undefined global functions or variables:
  ncbi_tax_id
* 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: biomart_query
> ### Title: Query the Ensembl BioMart web service
> ### Aliases: biomart_query
> 
> ### ** Examples
> 
> cel_genes <- biomart_query(
+     attrs = c("external_gene_name", "start_position", "end_position"),
+     gene = TRUE,
+     dataset = "celegans_gene_ensembl"
+ )
[2024-10-10 16:06:09] [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="celegans_gene_ensembl" interface="default" >
        <Attribute name="ensembl_gene_id"/>
        <Attribute name="external_gene_name"/>
        <Attribute name="start_position"/>
        <Attribute name="end_position"/>
    </Dataset>
</Query>
[2024-10-10 16:06:09] [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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-10-10 16:06:09] [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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-10-10 16:06:09] [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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-10 16:06:09] [INFO]    [OmnipathR] Cache item `a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c` version 1: status changed from `unknown` to `started`.
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c-1.rds`.
[2024-10-10 16:06:09] [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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-10-10 16:06:09] [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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-10-10 16:06:09] [TRACE]   [OmnipathR] HTTP 200
[2024-10-10 16:06:09] [WARN]    [OmnipathR] Failed to 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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` (attempt 1/3); error: `file` is not one of the supported inputs:
• A filepath or character vector of filepaths
• A connection or list of connections
• Literal or raw input
[2024-10-10 16:06:14] [TRACE]   [OmnipathR] Attempt 2/3: `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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-10-10 16:06:14] [TRACE]   [OmnipathR] HTTP 200
[2024-10-10 16:06:14] [WARN]    [OmnipathR] Failed to 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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` (attempt 2/3); error: `file` is not one of the supported inputs:
• A filepath or character vector of filepaths
• A connection or list of connections
• Literal or raw input
[2024-10-10 16:06:19] [TRACE]   [OmnipathR] Attempt 3/3: `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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-10-10 16:06:19] [TRACE]   [OmnipathR] HTTP 200
[2024-10-10 16:06:19] [ERROR]   [OmnipathR] Failed to 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=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` (attempt 3/3); error: `file` is not one of the supported inputs:
• A filepath or character vector of filepaths
• A connection or list of connections
• Literal or raw input
Error in vroom::vroom(file, delim = "\t", col_names = col_names, col_types = col_types,  : 
  `file` is not one of the supported inputs:
• A filepath or character vector of filepaths
• A connection or list of connections
• Literal or raw input
Calls: biomart_query ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
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, 4 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-10-10_1556/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-10-10 16:12:49 CEST ]