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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ViSEAGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ViSEAGO_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ViSEAGO/DESCRIPTION’ ... OK
* this is package ‘ViSEAGO’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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’
  Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
  Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  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 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 ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOterms_heatmap,GO_SS: no visible binding for global variable ‘GO.ID’
MDSplot,ANY: no visible binding for global variable ‘GO.cluster’
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 ‘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 : <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.ID GO.cluster IC Id N NES ONTOLOGY
  Significant_genes genes_frequency leadingEdge log2err nMoreExtreme
  padj pathway pval size
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  overLapper.Rd: upset
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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    516Kb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 4 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ViSEAGO.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ViSEAGO
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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’
Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ 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’
Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ 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’
Warning: replacing previous import ‘dendextend::cutree’ by ‘stats::cutree’ when loading ‘ViSEAGO’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘ViSEAGO’
** testing if installed package keeps a record of temporary installation path
* DONE (ViSEAGO)