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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ViSEAGO_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.16.0’
* 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 ‘ViSEAGO’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
See ‘/home/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    extdata  10.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  GPL-3 bioconductor.org
Standardizable: FALSE
* 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 ... WARNING
'library' or 'require' call not declared from: ‘topGO’
'library' or 'require' call to ‘topGO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘processx’
  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 ... NOTE
annotate,character-genomic_ressource: warning in getBM(attributes =
  c("ensembl_gene_id", "go_id", "go_linkage_type", "namespace_1003"),
  filters = unlist(go_filter[grep("with GO ID", ignore.case = TRUE,
  go_filter$description), "name", with = FALSE]), value = TRUE, mart =
  myspecies): partial argument match of 'value' to 'values'
compute_SS_distances,ANY-character: warning in select(GO.db, keys =
  onto$values, column = "TERM"): partial argument match of 'column' to
  'columns'
merge_enrich_terms,list : genes_symbols_add: warning in
  getBM(attributes = c("ensembl_gene_id", "external_gene_name"), value
  = TRUE, mart = myspecies): partial argument match of 'value' to
  'values'
GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’
MDSplot,ANY: no visible binding for global variable ‘text’
MDSplot,ANY: no visible binding for global variable ‘GO.cluster’
Upset,ANY: no visible global function definition for ‘png’
Upset,ANY: no visible global function definition for ‘dev.off’
annotate,character-genomic_ressource: no visible global function
  definition for ‘.’
annotate,character-genomic_ressource: no visible binding for global
  variable ‘ENTREZID’
annotate,character-genomic_ressource: no visible binding for global
  variable ‘GO’
annotate,character-genomic_ressource: no visible binding for global
  variable ‘EVIDENCE’
annotate,character-genomic_ressource: no visible binding for global
  variable ‘ONTOLOGY’
compute_SS_distances,ANY-character: no visible binding for global
  variable ‘N’
compute_SS_distances,ANY-character: no visible binding for global
  variable ‘IC’
merge_enrich_terms,list : genes_symbols_add : esummary : <anonymous>:
  no visible binding for global variable ‘start’
merge_enrich_terms,list : genes_symbols_add : esummary : <anonymous>:
  no visible binding for global variable ‘end’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘pval’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘pathway’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘Id’
merge_enrich_terms,list : <anonymous>: no visible global function
  definition for ‘.’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘padj’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘nMoreExtreme’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘ES’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘NES’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘size’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘genes_frequency’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘log2err’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘leadingEdge’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘Significant_genes’
merge_enrich_terms,list : <anonymous>: no visible binding for global
  variable ‘GO.ID’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
  ‘genes_frequency’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
  ‘leadingEdge’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
  ‘size’
runfgsea,ANY-gene2GO-character: no visible binding for global variable
  ‘pathway’
Undefined global functions or variables:
  . ENTREZID ES EVIDENCE GO GO.ID GO.cluster IC Id N NES ONTOLOGY
  Significant_genes dev.off end genes_frequency leadingEdge log2err
  nMoreExtreme padj pathway png pval size start text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "text")
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  myGOs.RData    876Kb    517Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SS_choice.Rmd’ using ‘UTF-8’... failed
  ‘ViSEAGO.Rmd’ using ‘UTF-8’... failed
  ‘fgsea_alternative.Rmd’ using ‘UTF-8’... OK
  ‘mouse_bioconductor.Rmd’ using ‘UTF-8’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘SS_choice.Rmd’
  ...
+     comment = .... [TRUNCATED] 

> data(myGOs, package = "ViSEAGO")

> Resnik_clusters_wardD2 <- ViSEAGO::GOterms_heatmap(myGOs, 
+     showIC = TRUE, showGOlabels = TRUE, GO.tree = list(tree = list(distance = "Resnik", .... [TRUNCATED] 

  When sourcing ‘SS_choice.R’:
Error: Argument dendro must have class hclust.
Execution halted
when running code in ‘ViSEAGO.Rmd’
  ...
	‘/tmp/RtmpDeIyeD/downloaded_packages’

> background <- scan("background.txt", quiet = TRUE, 
+     what = "")
Warning in file(file, "r") :
  cannot open file 'background.txt': No such file or directory

  When sourcing ‘ViSEAGO.R’:
Error: cannot open the connection
Execution halted

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ViSEAGO
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘ViSEAGO’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘data.table::set’ by ‘dendextend::set’ when loading ‘ViSEAGO’
** testing if installed package keeps a record of temporary installation path
* DONE (ViSEAGO)