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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings fenr_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘fenr/DESCRIPTION’ ... OK
* this is package ‘fenr’ version ‘1.8.0’
* 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 loading without being on the library search path ... 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_reactome
> ### Title: Get functional term data from Reactome
> ### Aliases: fetch_reactome
> 
> ### ** Examples
> 
> reactome_data <- fetch_reactome("Saccharomyces cerevisiae", on_error = "warn")
Warning: download failed
  web resource path: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’
  local file path: ‘/home/biocbuild/.cache/R/fenr/1400071ba5734_Ensembl2Reactome_PE_Pathway.txt’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Failure when receiving data from the peer [reactome.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
Warning: bfcadd() failed; resource removed
  rid: BFC2
  fpath: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’
  reason: download failed
Error in .util_download(x, rid[i], proxy, progress, config, "bfcadd()",  : 
  bfcadd() failed; see warnings()
Calls: fetch_reactome ... cache_path -> <Anonymous> -> <Anonymous> -> .util_download
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
fetch_go   11.954  0.795 650.251
fetch_kegg  1.228  0.006  20.671
* 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 2 | PASS 302 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL fenr
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘fenr’ ...
** this is package ‘fenr’ version ‘1.8.0’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 2 | PASS 302 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test_bp.R:9:1', 'test_go.R:56:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_reactome.R:62:3'): Correct Reactome Ensembl from yeast ─────────
<curl_error_recv_error/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: 0x6088ed9cc9a0>), raw(0), 131071L)`: Failure when receiving data from the peer [reactome.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
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 2 | PASS 302 ]
Error:
! Test failures.
Execution halted