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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings KEGGREST_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/KEGGREST.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.49.0’
* 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 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 ... ERROR
Running examples in ‘KEGGREST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mark.pathway.by.objects
> ### Title: Client-side interface to obtain an url for a KEGG pathway
> ###   diagram with a given set of genes marked
> ### Aliases: mark.pathway.by.objects color.pathway.by.objects
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  url <- mark.pathway.by.objects(
+     "path:eco00260", c("eco:b0002", "eco:c00263")
+ )
Error in .get.kegg.url(url) : 
  Not Found (HTTP 404). Failed to GET KEGG pathway URL.
Calls: mark.pathway.by.objects -> .get.kegg.url -> stop_for_status
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
listDatabases 0.638  0.059  16.184
keggList      0.534  0.047  15.716
keggLink      0.314  0.027   7.245
* 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 .get.kegg.url(url) : 
    Not Found (HTTP 404). Failed to GET KEGG pathway URL.
  
  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: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL KEGGREST
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘KEGGREST’ ...
** this is package ‘KEGGREST’ version ‘1.49.0’
** 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)

R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 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.

> BiocGenerics:::testPackage("KEGGREST")
Timing stopped at: 0.011 0.001 1.279
Error in .get.kegg.url(url) : 
  Not Found (HTTP 404). Failed to GET KEGG pathway URL.


RUNIT TEST PROTOCOL -- Thu Jun 12 21:35:43 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 .get.kegg.url(url) : 
  Not Found (HTTP 404). Failed to GET KEGG pathway URL.

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