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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_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/fenr.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fenr/DESCRIPTION’ ... OK
* this is package ‘fenr’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
fetch_reactome 6.880  0.500   7.639
fetch_go       5.967  0.209  15.297
fetch_kegg     0.466  0.049  19.892
fetch_wiki     0.041  0.002  11.601
* 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:
    3. │   ├─dplyr::distinct(...)
    4. │   ├─dplyr::filter(...)
    5. │   ├─dplyr::select(...)
    6. │   ├─dplyr::mutate(...)
    7. │   ├─dplyr::filter(...)
    8. │   └─readr::read_tsv(lpath, col_names = colms, show_col_types = FALSE)
    9. │     └─vroom::vroom(...)
   10. │       └─vroom:::vroom_(...)
   11. ├─base (local) `<fn>`(`<curl>`, `<raw>`, 131071L)
   12. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 296 ]
  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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.23-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/4.6-arm64/Resources/library’
* installing *source* package ‘fenr’ ...
** this is package ‘fenr’ version ‘1.9.0’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")






Saving _problems/test_reactome-62.R
[ FAIL 1 | WARN 0 | SKIP 3 | PASS 296 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_bp.R:9:1', 'test_go.R:56:1', 'test_reactome.R:91:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_reactome.R:62:3'): Correct Reactome Ensembl from yeast ─────────
<curl_error_partial_file/curl_error/error/condition>
Error in `(function (con, what, n = 1L, size = NA_integer_, signed = TRUE, endian = .Platform$endian)  {     if (!endian %in% c("big", "little", "swap"))          stop("invalid 'endian' argument")     if (is.character(con)) {         con <- file(con, "rb")         on.exit(close(con))     }     swap <- endian != .Platform$endian     if (!is.character(what) || is.na(what) || length(what) != 1L || !any(what == c("numeric", "double", "integer", "int", "logical", "complex", "character", "raw")))          what <- typeof(what)     .Internal(readBin(con, what, n, size, signed, swap)) })(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x11f6e19e0>), raw(0), 131071L)`: Transferred a partial file [reactome.org]:
transfer closed with outstanding read data remaining
Backtrace:
     ▆
  1. ├─fenr::fetch_reactome(...) at test_reactome.R:62:3
  2. │ └─fenr:::fetch_reactome_ensembl_genes(...)
  3. │   ├─dplyr::distinct(...)
  4. │   ├─dplyr::filter(...)
  5. │   ├─dplyr::select(...)
  6. │   ├─dplyr::mutate(...)
  7. │   ├─dplyr::filter(...)
  8. │   └─readr::read_tsv(lpath, col_names = colms, show_col_types = FALSE)
  9. │     └─vroom::vroom(...)
 10. │       └─vroom:::vroom_(...)
 11. ├─base (local) `<fn>`(`<curl>`, `<raw>`, 131071L)
 12. └─curl:::raise_libcurl_error(...)

[ FAIL 1 | WARN 0 | SKIP 3 | PASS 296 ]
Error:
! Test failures.
Execution halted