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This page was generated on 2025-09-06 12:08 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 1098/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGREST 1.49.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/KEGGREST
git_branch: devel
git_last_commit: 6125ec8
git_last_commit_date: 2025-06-18 12:02:37 -0400 (Wed, 18 Jun 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 KEGGREST on taishan

To the developers/maintainers of the KEGGREST package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/KEGGREST.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: KEGGREST
Version: 1.49.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings KEGGREST_1.49.1.tar.gz
StartedAt: 2025-09-05 08:46:54 -0000 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 08:49:58 -0000 (Fri, 05 Sep 2025)
EllapsedTime: 184.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: KEGGREST.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings KEGGREST_1.49.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/KEGGREST.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 ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.49.1’
* 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 ‘KEGGREST’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
listDatabases 0.605  0.017   7.481
keggList      0.503  0.016   7.863
keggLink      0.338  0.027   6.857
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘KEGGREST_unit_tests.R’
 ERROR
Running the tests in ‘tests/KEGGREST_unit_tests.R’ failed.
Last 13 lines of output:
  1 Test Suite : 
  KEGGREST RUnit Tests - 12 test functions, 1 error, 0 failures
  ERROR in test_mark_and_color_pathways_by_objects: Error in curl::curl_fetch_memory(url, handle = handle) : 
    Failure when receiving data from the peer [www.kegg.jp]:
  Recv failure: Connection reset by peer
  
  Test files with failing tests
  
     test_KEGGREST.R 
       test_mark_and_color_pathways_by_objects 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  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/KEGGREST.Rcheck/00check.log’
for details.


Installation output

KEGGREST.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘KEGGREST’ ...
** this is package ‘KEGGREST’ version ‘1.49.1’
** using staged installation
** R
** inst
** 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 (KEGGREST)

Tests output

KEGGREST.Rcheck/tests/KEGGREST_unit_tests.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.

> BiocGenerics:::testPackage("KEGGREST")
Timing stopped at: 0.005 0.004 4.327
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failure when receiving data from the peer [www.kegg.jp]:
Recv failure: Connection reset by peer


RUNIT TEST PROTOCOL -- Fri Sep  5 08:49:55 2025 
*********************************************** 
Number of test functions: 12 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
KEGGREST RUnit Tests - 12 test functions, 1 error, 0 failures
ERROR in test_mark_and_color_pathways_by_objects: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failure when receiving data from the peer [www.kegg.jp]:
Recv failure: Connection reset by peer

Test files with failing tests

   test_KEGGREST.R 
     test_mark_and_color_pathways_by_objects 


Error in BiocGenerics:::testPackage("KEGGREST") : 
  unit tests failed for package KEGGREST
Execution halted

Example timings

KEGGREST.Rcheck/KEGGREST-Ex.timings

nameusersystemelapsed
keggCompounds0.0410.0120.593
keggConv0.2830.0044.609
keggFind0.0590.0012.590
keggGet1.3140.0842.540
keggInfo0.0290.0011.424
keggLink0.3380.0276.857
keggList0.5030.0167.863
listDatabases0.6050.0177.481
mark.pathway.by.objects0.0180.0003.158