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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SurfR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SurfR_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SurfR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SurfR’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘SurfR’ 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 ‘SurfR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Enrichment_barplot
> ### Title: Enrichment_barplot
> ### Aliases: Enrichment_barplot
> 
> ### ** Examples
> 
> dbs <- c("GO_Biological_Process_2021")
> dfList <- list()
> if (requireNamespace("enrichR", quietly = TRUE)) {
+     up_genes <- c("RUNX1", "DLK1", "TOP2A", "EPCAM", "GATA1", "KDR")
+     dfList[["fdr_up"]] <- enrichR::enrichr(up_genes, dbs)
+     dw_genes <- c("CD275", "COL1A1", "COL1A2","LUM", "SOX9")
+     dfList[["fdr_down"]] <- enrichR::enrichr(dw_genes, dbs)
+     # Plot upregulated genes
+     Enrichment_barplot(dfList,
+                        enrich.databases = dbs,
+                        p_adj = 0.01, num_term = 5, cond = "UP")
+     # Plot downregulated genes
+     #Enrichment_barplot(dfList,
+     #                   enrich.databases = dbs,
+     #                   p_adj = 0.01, num_term = 5, cond = "DOWN")
+ } else {
+     print("example requires enrichR package")
+ }
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2021... Done.
Parsing results... Done.
Uploading data to Enrichr... Done.
  Querying GO_Biological_Process_2021... Done.
Parsing results... Done.
Error in Enrichment_barplot(dfList, enrich.databases = dbs, p_adj = 0.01,  : 
  object 'pathways.dataframe' not found
Calls: Enrichment_barplot -> head
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/SurfR.Rcheck/00check.log’
for details.