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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings SWATH2stats_1.41.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.41.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘aLFQ’
* 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 ‘SWATH2stats’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘SWATH2stats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: load_mart
> ### Title: Establish connection to biomaRt database
> ### Aliases: load_mart
> 
> ### ** Examples
> 
> {
+  data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"),
+                           Abundance = c(100, 3390, 43423))
+  mart <- convert_protein_ids(data_table)
+  }
Error in checkDataset(dataset = dataset, mart = mart) : 
  The given dataset: hsapiens_gene_ensembl, is not valid.  Correct dataset names can be obtained with the listDatasets() function.
Calls: convert_protein_ids ... load_mart -> useMart -> .useMart -> useDataset -> checkDataset
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── Error ('test_biomart.R:6:3'): convert_ids ───────────────────────────────────
  Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
  Look at ?useEnsembl for details on how to try a mirror site.
  Backtrace:
      ▆
   1. └─SWATH2stats::convert_protein_ids(data_table) at test_biomart.R:6:3
   2.   └─SWATH2stats::load_mart(species, host, mart)
   3.     └─biomaRt::useMart(mart, dataset = dataset.mart, host = ensembl.path)
   4.       └─biomaRt:::.useMart(...)
   5.         └─biomaRt:::.listMarts(...)
  
  [ FAIL 1 | WARN 70 | SKIP 0 | PASS 111 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL SWATH2stats
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘SWATH2stats’ ...
** this is package ‘SWATH2stats’ version ‘1.41.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SWATH2stats)

R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> library(testthat)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
Saving _problems/test_biomart-6.R
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
[ FAIL 1 | WARN 70 | SKIP 0 | PASS 111 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_biomart.R:6:3'): convert_ids ───────────────────────────────────
Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
Backtrace:
    ▆
 1. └─SWATH2stats::convert_protein_ids(data_table) at test_biomart.R:6:3
 2.   └─SWATH2stats::load_mart(species, host, mart)
 3.     └─biomaRt::useMart(mart, dataset = dataset.mart, host = ensembl.path)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt:::.listMarts(...)

[ FAIL 1 | WARN 70 | SKIP 0 | PASS 111 ]
Error:
! Test failures.
Execution halted