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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:ggkegg.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ggkegg_1.3.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggkegg/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggkegg’ version ‘1.3.1’
* 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 ‘ggkegg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... ERROR
Running examples in ‘ggkegg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: append_cp
> ### Title: append_cp
> ### Aliases: append_cp
> 
> ### ** Examples
> 
> graph <- create_test_pathway()
> nodes <- graph |> data.frame()
> if (require("clusterProfiler")) {
+     cp <- enrichKEGG(nodes$name |>
+             strsplit(":") |>
+             vapply("[", 2, FUN.VALUE="character"))
+     ## This append graph node logical value whether the 
+     ## enriched genes are in pathway
+     graph <- graph |> mutate(cp=append_cp(cp, pid="hsa05322"))
+ }
Loading required package: clusterProfiler

clusterProfiler v4.13.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: ‘clusterProfiler’

The following object is masked from ‘package:igraph’:

    simplify

The following object is masked from ‘package:stats’:

    filter

Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Warning in file(con, "r") :
  URL 'https://rest.kegg.jp/link/hsa/pathway': Timeout of 9000 seconds was reached
Error in file(con, "r") : 
  cannot open the connection to 'https://rest.kegg.jp/link/hsa/pathway'
Calls: enrichKEGG ... eval -> <Anonymous> -> do.call -> <Anonymous> -> file
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ggkegg.Rcheck/00check.log’
for details.