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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EnrichmentBrowser_2.40.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.40.0’
* 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 ‘EnrichmentBrowser’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
Undefined global functions or variables:
  go_linkage_type
* 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:
  compileGRN.Rd: KEGGPathway-class, pathwayDatabases, pathways,
    parseKGML
  deAna.Rd: SummarizedExperiment-class, colData, filterByExpr, rowData,
    voom, eBayes, glmQLFit
  downloadPathways.Rd: keggList, keggGet, KEGGPathway-class, parseKGML
  eaBrowse.Rd: DataFrame-class
  ebrowser.Rd: SummarizedExperiment-class, assays, colData, rowData,
    kegg.species.code, normalizeBetweenArrays, lmFit,
    normalizeWithinArrays
  getGenesets.Rd: GeneSetCollection-class, DataFrame-class, keggList,
    keggLink
  ggeaGraph.Rd: SummarizedExperiment-class
  idMap.Rd: SummarizedExperiment-class, GeneSetCollection-class,
    rowData, mapIds, keytypes
  import.Rd: SummarizedExperiment-class, EList-class, DGEList-class,
    TopTags-class, voom, eBayes, glmQLFit
  isAvailable.Rd: install
  nbea.Rd: SummarizedExperiment-class
  normalize.Rd: SummarizedExperiment-class, normalizeBetweenArrays,
    filterByExpr, normalizeWithinArrays, cpm, estimateDisp, voom
  probe2gene.Rd: SummarizedExperiment-class, metadata, rowData, mapIds
  readSE.Rd: SummarizedExperiment-class
  sbea.Rd: SummarizedExperiment-class
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ebrowser    101.874 23.121 170.785
getGenesets  16.277  0.852  28.804
eaBrowse      9.378  0.936  14.466
import        5.208  0.183   7.192
ggeaGraph     5.003  0.091   6.951
deAna         4.214  0.250   6.134
compileGRN    3.989  0.219   6.115
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.