##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SWATH2stats_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.29.0’
* 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 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Warning message:
  In utils::packageDescription(basename(dir), dirname(dir)) :
    no package 'SWATH2stats' was found
* 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 loading without being on the library search path ... WARNING
Error in library(SWATH2stats, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘SWATH2stats’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... NOTE
checkRd: (-1) sample_annotation.Rd:29: Escaped LaTeX specials: \_
* 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 ... SKIPPED
* 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:
    3.     └─biomaRt::useMart(mart, dataset = dataset.mart, host = ensembl.path)
    4.       └─biomaRt:::.useMart(...)
    5.         └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
    6.           └─biomaRt:::.getAttributes(mart, verbose = verbose)
    7.             └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
    8.               └─biomaRt:::bmRequest(...)
    9.                 └─httr::GET(...)
   10.                   └─httr:::request_perform(req, hu$handle$handle)
   11.                     ├─httr:::request_fetch(req$output, req$url, handle)
   12.                     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   13.                       └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 74 | 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 ...
  ‘SWATH2stats_example_script.Rmd’ using ‘UTF-8’... OK
  ‘SWATH2stats_vignette.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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"
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 111 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_biomart.R:6'): convert_ids ─────────────────────────────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [www.ensembl.org:80] Operation timed out after 10000 milliseconds with 425942 bytes received
Backtrace:
     ▆
  1. └─SWATH2stats::convert_protein_ids(data_table) at 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::useDataset(mart = mart, dataset = dataset, verbose = verbose)
  6.           └─biomaRt:::.getAttributes(mart, verbose = verbose)
  7.             └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes")
  8.               └─biomaRt:::bmRequest(...)
  9.                 └─httr::GET(...)
 10.                   └─httr:::request_perform(req, hu$handle$handle)
 11.                     ├─httr:::request_fetch(req$output, req$url, handle)
 12.                     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 13.                       └─curl::curl_fetch_memory(url, handle = handle)

[ FAIL 1 | WARN 74 | SKIP 0 | PASS 111 ]
Error: Test failures
Execution halted