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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings SWATH2stats_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.22.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
load_mart 2.385  0.332  18.427
* 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 in `bmRequest(request = request, httr_config = httr_config, verbose = verbose)`: Gateway Timeout (HTTP 504).
  Backtrace:
      █
   1. └─SWATH2stats::convert_protein_ids(data_table) test_biomart.R:6:2
   2.   └─SWATH2stats::load_mart(species, host, mart)
   3.     └─biomaRt::useMart(mart, dataset = dataset.mart, host = ensembl.path)
   4.       └─biomaRt:::.useMart(...)
   5.         └─biomaRt::listMarts(...)
   6.           └─biomaRt:::.listMarts(...)
   7.             └─biomaRt:::bmRequest(...)
   8.               └─httr::stop_for_status(result)
  
  [ FAIL 1 | WARN 73 | SKIP 0 | PASS 111 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL SWATH2stats
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘SWATH2stats’ ...
** 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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_biomart.R:6:3): convert_ids ─────────────────────────────────────
<http_504/http_500/http_error/error/condition>
Error in `bmRequest(request = request, httr_config = httr_config, verbose = verbose)`: Gateway Timeout (HTTP 504).
Backtrace:
    █
 1. └─SWATH2stats::convert_protein_ids(data_table) test_biomart.R:6:2
 2.   └─SWATH2stats::load_mart(species, host, mart)
 3.     └─biomaRt::useMart(mart, dataset = dataset.mart, host = ensembl.path)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt::listMarts(...)
 6.           └─biomaRt:::.listMarts(...)
 7.             └─biomaRt:::bmRequest(...)
 8.               └─httr::stop_for_status(result)

[ FAIL 1 | WARN 73 | SKIP 0 | PASS 111 ]
Error: Test failures
Execution halted