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This page was generated on 2024-05-22 11:35:58 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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 1467/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.12.0  (landing page)
Denes Turei
Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: 330f65c
git_last_commit_date: 2024-04-30 11:18:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for OmnipathR on palomino3


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.

raw results

Summary

Package: OmnipathR
Version: 3.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OmnipathR_3.12.0.tar.gz
StartedAt: 2024-05-22 04:43:32 -0400 (Wed, 22 May 2024)
EndedAt: 2024-05-22 04:51:35 -0400 (Wed, 22 May 2024)
EllapsedTime: 483.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OmnipathR_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-22 04:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:43:58] [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
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:12] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:12] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-22 04:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:44:13] [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: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2024-05-22 04:50:44] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2024-05-22 04:50:45] [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>
[2024-05-22 04:50:45] [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`.
[2024-05-22 04:50:45] [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`
[2024-05-22 04:50:45] [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`.
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:45] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-05-22 04:50:45] [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`
[2024-05-22 04:50:45] [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`
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-05-22 04:50:45] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:50:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:45] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2024-05-22 04:50:45] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <html>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <head>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <style>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] html,
[2024-05-22 04:50:45] [WARN]    [OmnipathR] body {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] padding: 0;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] margin: 0;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] height: 100%;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] body {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] display: grid;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] font-size: 90%;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] h1 {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] font-size: 1.5rem;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] h2 {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] font-size: 1.2rem;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] h3 {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] font-size: 1.1rem;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] header {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] grid-row: header;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] padding: 5px;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] height: 60px;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] background-color: #333366;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] header img {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] width: 185px;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] height: 45px
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] main {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] grid-row: main;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] padding: 20px;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] footer {
[2024-05-22 04:50:45] [WARN]    [OmnipathR] grid-row: footer;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] padding: 0 20px;
[2024-05-22 04:50:45] [WARN]    [OmnipathR] }
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </style>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </head>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <body>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <header>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </header>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <main>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <p>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] The Ensembl websites and REST servers are currently unavailable as we apply updates.
[2024-05-22 04:50:45] [WARN]    [OmnipathR] Our archive sites, FTP site and public MySQL servers are unaffected.
[2024-05-22 04:50:45] [WARN]    [OmnipathR] Please try again shortly.
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </p>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <p>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </p>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </main>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <footer>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </footer>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </body>
[2024-05-22 04:50:45] [WARN]    [OmnipathR] </html>
[2024-05-22 04:50:45] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 67 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Contains 4 files.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:13] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-21 16:21:16] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:48] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Contains 37 files.
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-22 04:50:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:48] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-22 04:50:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-22 04:50:49] [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 
  11.23    1.68   29.11

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.030.000.03
all_uniprots0.020.000.01
ancestors0.000.010.02
annotated_network1.840.245.95
annotation_categories74.77 0.0375.48
biomart_query0.220.060.47
bioplex10.030.000.03
bioplex20.010.000.02
bioplex30.020.020.03
bioplex_all0.010.000.02
bioplex_hct116_10.000.010.01
bma_motif_es0.420.041.17
bma_motif_vs0.110.000.50
collectri111.92 1.78113.83
common_name0.030.000.03
consensuspathdb_download000
consensuspathdb_raw_table0.020.000.01
curated_ligand_receptor_interactions 4.75 0.3710.57
curated_ligrec_stats29.86 2.2773.42
database_summary1.310.062.11
descendants0.020.000.01
dorothea67.29 0.9169.00
ensembl_dataset0.020.000.02