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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings EnrichmentBrowser_2.39.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/EnrichmentBrowser.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.39.1’
* 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: getGenesets
> ### Title: Definition of gene sets according to different sources
> ### Aliases: getGenesets get.go.genesets get.kegg.genesets
> ###   parse.genesets.from.GMT showAvailableSpecies showAvailableCollections
> ###   writeGMT
> 
> ### ** Examples
> 
> 
>     # (1) Typical usage for gene set enrichment analysis with GO:
>     # Biological process terms based on BioC annotation (for human)
>     go.gs <- getGenesets(org = "hsa", db = "go")
>     
>     # eq.:  
>     # go.gs <- getGenesets(org = "hsa", db = "go", onto = "BP", mode = "GO.db")
>     # (2) Defining gene sets according to KEGG  
>     kegg.gs <- getGenesets(org = "hsa", db = "kegg")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [rest.kegg.jp]:
Connection timed out after 10002 milliseconds
Calls: getGenesets ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ebrowser 686.257 26.751 753.096
eaBrowse   9.370  0.521  10.108
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL EnrichmentBrowser
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘EnrichmentBrowser’ ...
** this is package ‘EnrichmentBrowser’ version ‘2.39.1’
** 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)