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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings YAPSA_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/YAPSA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘YAPSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘YAPSA’ version ‘1.31.0’
* 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 ‘YAPSA’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘YAPSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_gene_list_for_pathway
> ### Title: Build a gene list for a given pathway name
> ### Aliases: build_gene_list_for_pathway
> 
> ### ** Examples
> 
>    species <- "hsa"
>    gene_lists_meta_df <- data.frame(
+      name=c("BER","NHEJ","MMR"),
+      explanation=c("base excision repair",
+                    "non homologous end joining",
+                    "mismatch repair"))
>    number_of_pathways <- dim(gene_lists_meta_df)[1]
>    gene_lists_list <- list()
>    for (i in seq_len(number_of_pathways)) {
+      temp_list <- 
+        build_gene_list_for_pathway(gene_lists_meta_df$explanation[i],
+                                    species)
+      gene_lists_list <- c(gene_lists_list,list(temp_list))
+    }
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).
Calls: build_gene_list_for_pathway -> keggFind -> .getUrl -> stop_for_status
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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/YAPSA.Rcheck/00check.log’
for details.