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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:KEGGlincs.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings KEGGlincs_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/KEGGlincs.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘KEGGlincs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGlincs’ version ‘1.28.0’
* 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 ‘KEGGlincs’ 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 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 ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
* 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 ‘KEGGlincs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edge_mapping_info
> ### Title: Prepare edges for mapping
> ### Aliases: edge_mapping_info
> 
> ### ** Examples
> 
> p53_KGML <- get_KGML("hsa04115")
> p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
> 
> #Default; no data added to edges:
> 
> p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
> p53_edge_mapping_info <- edge_mapping_info(p53_edges) 
> 
> #If data is added to edges as additional attribute[s]:
> 
> p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 
+                                "HA1E", data_type = "100_bing")
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/KEGGlincs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL KEGGlincs
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘KEGGlincs’ ...
** 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 (KEGGlincs)