##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings EnrichmentBrowser_2.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/EnrichmentBrowser.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.41.0’
* 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘EnrichmentBrowser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ebrowser
> ### Title: Seamless navigation through enrichment analysis results
> ### Aliases: ebrowser
> 
> ### ** Examples
> 
> 
>     # expression data from file
>     exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
>     cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
>     rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
>     
>     # getting all human KEGG gene sets
>     # hsa.gs <- getGenesets(org="hsa", db="kegg")
>     gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
>     hsa.gs <- getGenesets(gs.file)
> 
>     # output destination 
>     out.dir <- configEBrowser("OUTDIR.DEFAULT") 
> 
>     # set-based enrichment analysis
>     ebrowser( meth="ora", perm=0,
+             exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, 
+             gs=hsa.gs, org="hsa", nr.show=3,
+             out.dir=out.dir, report.name="oraReport")
Read expression data ...
Normalize ...
Excluding 211 genes not satisfying min.cpm threshold
Corresponding software package not found: EDASeq
Make sure that you have it installed.
Bioconductor version 3.23 (BiocManager 1.30.26), R Under development (unstable)
  (2025-10-20 r88955)
Installing package(s) 'BiocVersion', 'EDASeq'
package 'EDASeq' is not available for Bioconductor version '3.23'

A version of this package for your version of R might be available elsewhere,
  see the ideas at
  https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocVersion_3.23.1.tar.gz'
Content type 'application/x-gzip' length 990 bytes
==================================================
downloaded 990 bytes

* installing *source* package ‘BiocVersion’ ...
** this is package ‘BiocVersion’ version ‘3.23.1’
** using staged installation
** help
*** installing help indices
** building package indices
** 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 (BiocVersion)

The downloaded source packages are in
	'/tmp/RtmpAwtiiv/downloaded_packages'
Error in betweenLaneNormalization(assay(se), which = norm.method) : 
  could not find function "betweenLaneNormalization"
Calls: ebrowser -> normalize
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
eaBrowse  7.5  0.482   7.987
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL EnrichmentBrowser
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘EnrichmentBrowser’ ...
** this is package ‘EnrichmentBrowser’ version ‘2.41.0’
** 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)