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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:KEGGREST.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings KEGGREST_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/KEGGREST.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘KEGGREST/DESCRIPTION’ ... OK
* this is package ‘KEGGREST’ version ‘1.39.0’
* 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 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 R 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 ... WARNING
Error in library(KEGGREST, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘KEGGREST’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* 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 ... NOTE
checkRd: (-1) mark.pathway.by.objects.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) mark.pathway.by.objects.Rd:39: Escaped LaTeX specials: \#
* 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 ... SKIPPED
* 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:
  
     test_KEGGREST.R 
       test_keggConv 
       test_keggFind 
       test_keggGet 
       test_keggGet_2 
       test_keggInfo 
       test_keggLink 
       test_keggList 
       test_listDatabases 
  
  
  Error in BiocGenerics:::testPackage("KEGGREST") : 
    unit tests failed for package KEGGREST
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘KEGGREST-vignette.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/KEGGREST.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL KEGGREST
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘KEGGREST’ ...
** 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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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: 0.397 0.012 191.2
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.17 0 10
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.184 0 10
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 6.572 2.228 176.6
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.156 0 10
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.171 0 10
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.164 0 10
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
Timing stopped at: 0.596 1.362 619.8
Error in readLines(url) : cannot read from connection
In addition: Warning message:
In readLines(url) :
  URL 'https://rest.kegg.jp/list/organism': Timeout of 600 seconds was reached
No encoding supplied: defaulting to UTF-8.


RUNIT TEST PROTOCOL -- Sun Jan 29 02:34:43 2023 
*********************************************** 
Number of test functions: 11 
Number of errors: 8 
Number of failures: 0 

 
1 Test Suite : 
KEGGREST RUnit Tests - 11 test functions, 8 errors, 0 failures
ERROR in test_keggConv: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggFind: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggGet: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggGet_2: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggInfo: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggLink: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_keggList: Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [rest.kegg.jp] SSL connection timeout
ERROR in test_listDatabases: Error in readLines(url) : cannot read from connection

Test files with failing tests

   test_KEGGREST.R 
     test_keggConv 
     test_keggFind 
     test_keggGet 
     test_keggGet_2 
     test_keggInfo 
     test_keggLink 
     test_keggList 
     test_listDatabases 


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