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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fenr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fenr_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/fenr.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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fenr/DESCRIPTION’ ... OK
* this is package ‘fenr’ version ‘1.4.0’
* 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'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘fenr’ 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘fenr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fetch_kegg
> ### Title: Get functional term data from KEGG
> ### Aliases: fetch_kegg
> 
> ### ** Examples
> 
> kegg_data <- fetch_kegg("mge", on_error = "warn")
Error in `purrr::map()`:
ℹ In index: 1.
ℹ With name: 1.
Caused by error in `purrr::map()`:
ℹ In index: 10.
Caused by error:
! vector memory limit of 96.0 Gb reached, see mem.maxVSize()
Backtrace:
     ▆
  1. ├─fenr::fetch_kegg("mge", on_error = "warn")
  2. │ └─fenr:::fetch_kegg_mapping(terms$term_id, batch_size, on_error)
  3. │   ├─purrr::list_rbind(...)
  4. │   │ └─purrr:::check_list_of_data_frames(x)
  5. │   │   └─vctrs::vec_check_list(x, call = error_call)
  6. │   │     └─vctrs::obj_check_list(x, ..., arg = arg, call = call)
  7. │   └─purrr::map(...)
  8. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  9. │       ├─purrr:::with_indexed_errors(...)
 10. │       │ └─base::withCallingHandlers(...)
 11. │       ├─purrr:::call_with_cleanup(...)
 12. │       └─fenr (local) .f(.x[[i]], ...)
 13. │         └─fenr:::parse_kegg_genes(st)
 14. │           ├─purrr::list_rbind(...)
 15. │           │ └─purrr:::check_list_of_data_frames(x)
 16. │           │   └─vctrs::vec_check_list(x, call = error_call)
 17. │           │     └─vctrs::obj_check_list(x, ..., arg = arg, call = call)
 18. │           └─purrr::map(...)
 19. │             └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 20. │               ├─purrr:::with_indexed_errors(...)
 21. │               │ └─base::withCallingHandlers(...)
 22. │               ├─purrr:::call_with_cleanup(...)
 23. │               └─fenr (local) .f(.x[[i]], ...)
 24. │                 ├─tibble::add_column(...)
 25. │                 │ └─base::is.data.frame(.data)
 26. │                 ├─dplyr::mutate(...)
 27. │                 ├─tidyr::separate(...)
 28. │                 └─tidyr:::separate.data.frame(...)
 29. │                   └─tidyr:::str_separate(...)
 30. │                     └─tidyr:::str_split_fixed(...)
 31. │                       └─tidyr:::simplifyPieces(pieces, n, fill == "left")
 32. └─base::.handleSimpleError(...)
 33.   └─purrr (local) h(simpleError(msg, call))
 34.     └─cli::cli_abort(...)
 35.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
          return(NULL)
      }
      pb$tick()
      st <- httr2::resp_body_string(resp$response)
      parse_kegg_genes(st)
  })`: ℹ In index: 1.
  ℹ With name: 1.
  Caused by error in `purrr::map()`:
  ℹ In index: 10.
  Caused by error:
  ! vector memory limit of 96.0 Gb reached, see mem.maxVSize()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 299 ]
  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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/fenr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL fenr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘fenr’ ...
** using staged installation
** R
** data
** 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 (fenr)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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)
> library(fenr)
> 
> test_check("fenr")
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 299 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_bp.R:9:1', 'test_go.R:84:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_kegg.R:18:3'): Parsing KEGG flat file ──────────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(entries, function(entry) {
    d <- unlist(stringr::str_split(entry, "\n"))
    n <- length(d)
    i <- 1
    while (i <= n & !(stringr::str_detect(d[i], "^ENTRY"))) i <- i + 
        1
    paths <- unlist(stringr::str_split(d[i], "\\s+"))
    pathway <- paths[2]
    i <- 1
    while (i <= n & !(stringr::str_detect(d[i], "^GENE"))) i <- i + 
        1
    if (i > n) 
        return(tibble::tibble(gene_id = character(0), gene_symbol = character(0)))
    genes <- stringr::str_remove(d[i], "GENE\\s+")
    i <- i + 1
    while (i <= n & stringr::str_detect(d[i], "^\\s+")) {
        genes <- c(genes, stringr::str_remove(d[i], "^\\s+"))
        i <- i + 1
    }
    tibble::add_column(dplyr::mutate(tidyr::separate(tibble::as_tibble_col(genes, 
        column_name = "data"), data, c("gene_id", "gene_symbol"), 
        sep = "\\s+", extra = "merge"), gene_symbol = dplyr::if_else(stringr::str_detect(gene_symbol, 
        ";"), stringr::str_remove(gene_symbol, ";.+$"), gene_id)), 
        term_id = pathway)
})`: ℹ In index: 1.
Caused by error:
! vector memory limit of 96.0 Gb reached, see mem.maxVSize()
Backtrace:
     ▆
  1. ├─fenr:::parse_kegg_genes(flat) at test_kegg.R:18:3
  2. │ ├─purrr::list_rbind(...)
  3. │ │ └─purrr:::check_list_of_data_frames(x)
  4. │ │   └─vctrs::vec_check_list(x, call = error_call)
  5. │ │     └─vctrs::obj_check_list(x, ..., arg = arg, call = call)
  6. │ └─purrr::map(...)
  7. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  8. │     ├─purrr:::with_indexed_errors(...)
  9. │     │ └─base::withCallingHandlers(...)
 10. │     ├─purrr:::call_with_cleanup(...)
 11. │     └─fenr (local) .f(.x[[i]], ...)
 12. │       ├─tibble::add_column(...)
 13. │       │ └─base::is.data.frame(.data)
 14. │       ├─dplyr::mutate(...)
 15. │       ├─tidyr::separate(...)
 16. │       └─tidyr:::separate.data.frame(...)
 17. │         └─tidyr:::str_separate(...)
 18. │           └─tidyr:::str_split_fixed(...)
 19. │             └─tidyr:::simplifyPieces(pieces, n, fill == "left")
 20. └─base::.handleSimpleError(...)
 21.   └─purrr (local) h(simpleError(msg, call))
 22.     └─cli::cli_abort(...)
 23.       └─rlang::abort(...)
── Error ('test_kegg.R:66:3'): Correct response from fetch_kegg ────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(batches, function(batch) {
    dbentries <- paste(batch, collapse = "+")
    resp <- http_request(get_kegg_url(), stringr::str_glue("get/{dbentries}"))
    if (resp$is_error) {
        catch_error("KEGG", resp, on_error)
        raise_error <<- TRUE
        return(NULL)
    }
    pb$tick()
    st <- httr2::resp_body_string(resp$response)
    parse_kegg_genes(st)
})`: ℹ In index: 1.
ℹ With name: 1.
Caused by error in `purrr::map()`:
ℹ In index: 10.
Caused by error:
! vector memory limit of 96.0 Gb reached, see mem.maxVSize()

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 299 ]
Error: Test failures
Execution halted