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### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EnrichmentBrowser.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings EnrichmentBrowser_2.37.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/EnrichmentBrowser.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'EnrichmentBrowser/DESCRIPTION' ... OK
* this is package 'EnrichmentBrowser' version '2.37.0'
* 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 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    92.84  12.48  105.45
getGenesets 15.88   0.79   21.02
eaBrowse    10.14   1.59   12.25
compileGRN   4.77   0.36    5.14
deAna        4.67   0.44    5.11
idMap        2.53   0.45    6.27
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/EnrichmentBrowser.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL EnrichmentBrowser
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'EnrichmentBrowser' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EnrichmentBrowser)