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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 724/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fenr 1.7.1  (landing page)
Marek Gierlinski
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/fenr
git_branch: devel
git_last_commit: 5c24ba4
git_last_commit_date: 2025-09-23 04:17:12 -0400 (Tue, 23 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for fenr on taishan

To the developers/maintainers of the fenr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fenr.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: fenr
Version: 1.7.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fenr_1.7.1.tar.gz
StartedAt: 2025-10-10 08:49:14 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 08:55:56 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 402.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: fenr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:fenr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fenr_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fenr/DESCRIPTION’ ... OK
* this is package ‘fenr’ version ‘1.7.1’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
fetch_go       29.711  0.721  43.235
fetch_reactome 10.640  0.656  64.397
fetch_kegg      1.042  0.005  18.067
fetch_wiki      0.103  0.000   8.533
* 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:
    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 1 | PASS 312 ]
  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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck/00check.log’
for details.


Installation output

fenr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL fenr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘fenr’ ...
** this is package ‘fenr’ version ‘1.7.1’
** 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)

Tests output

fenr.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")








[ FAIL 1 | WARN 0 | SKIP 1 | PASS 312 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_bp.R:9:1'

══ 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: 0x3eaecfd0>), 
    raw(0), 131071L)`: Failure when receiving data from the peer [reactome.org]:
OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 0
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 1 | PASS 312 ]
Error: Test failures
Execution halted

Example timings

fenr.Rcheck/fenr-Ex.timings

nameusersystemelapsed
enrichment_interactive000
fetch_bp0.3430.0081.765
fetch_go29.711 0.72143.235
fetch_go_species0.0210.0000.186
fetch_kegg 1.042 0.00518.067
fetch_kegg_species0.0810.0112.371
fetch_reactome10.640 0.65664.397
fetch_reactome_species0.0220.0002.040
fetch_terms_for_example000
fetch_wiki0.1030.0008.533
fetch_wiki_species0.010.000.31
functional_enrichment000
get_feature_terms000
get_term_features000
prepare_for_enrichment000
remove_cache000