##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SWATH2stats_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.35.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.19/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/PACKAGES'
 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 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 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’ ... OK
* 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 `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Could not resolve host: www.ensembl.org
Backtrace:
     ▆
  1. └─SWATH2stats::convert_protein_ids(data_table)
  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:::bmRequest(...)
  7.             └─httr2::req_perform(request)
  8.               └─base::tryCatch(...)
  9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.                     └─value[[3L]](cond)
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:
    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(...)
    6.           └─biomaRt:::bmRequest(...)
    7.             └─httr2::req_perform(request)
    8.               └─base::tryCatch(...)
    9.                 └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.                   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.                     └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 74 | SKIP 0 | PASS 111 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.