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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GSEABenchmarkeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GSEABenchmarkeR_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GSEABenchmarkeR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘GSEABenchmarkeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GSEABenchmarkeR’ version ‘1.30.0’
* 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 ‘GSEABenchmarkeR’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalRelevance: no visible binding for global variable ‘REL.SCORE’
Undefined global functions or variables:
  REL.SCORE
* 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:
  cacheResource.Rd: BiocFileCache-class
  evalRandomGS.Rd: sbeaMethods, nbeaMethods,
    SummarizedExperiment-class, sbea, nbea, BiocParallelParam-class,
    register
  evalRelevance.Rd: DataFrame-class, gsRanking
  evalTypeIError.Rd: sbeaMethods, nbeaMethods,
    SummarizedExperiment-class, sbea, nbea, BiocParallelParam-class,
    register
  loadEData.Rd: SummarizedExperiment-class, ExpressionSet-class
  maPreproc.Rd: ExpressionSet-class, BiocParallelParam-class,
    SummarizedExperiment-class
  readResults.Rd: sbeaMethods, nbeaMethods
  runDE.Rd: SummarizedExperiment-class, deAna, BiocParallelParam-class,
    rowData
  runEA.Rd: SummarizedExperiment-class, sbea, sbeaMethods, nbeaMethods,
    BiocParallelParam-class, nbea, register
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 ‘GSEABenchmarkeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: evalRandomGS
> ### Title: Evaluation of enrichment methods on random gene sets
> ### Aliases: evalRandomGS
> 
> ### ** Examples
> 
> 
>     # loading two datasets from the GEO2KEGG compendium
>     geo2kegg <- loadEData("geo2kegg", nr.datasets = 2)
Loading GEO2KEGG data compendium ...
> 
>     # only considering the first 1000 probes for demonstration
>     geo2kegg <- lapply(geo2kegg, function(d) d[1:1000,]) 
> 
>     # preprocessing and DE analysis for two of the datasets
>     geo2kegg <- maPreproc(geo2kegg)
Summarizing probe level expression ...
Corresponding annotation package not found: hgu133a.db
Make sure that you have it installed.
URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
cannot open URL 'https://bioconductor.org/config.yaml'
URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
cannot open URL 'http://bioconductor.org/config.yaml'
Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES':
  status was 'SSL connect error'
unable to access index for repository
  https://bioconductor.org/packages/3.22/data/experiment/src/contrib: cannot
  open URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
URL
  'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES':
  status was 'SSL connect error'
unable to access index for repository
  https://bioconductor.org/packages/3.22/workflows/src/contrib: cannot open URL
  'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES'
URL 'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES': status
  was 'SSL connect error'
unable to access index for repository
  https://bioconductor.org/packages/3.22/books/src/contrib: cannot open URL
  'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES'
Bioconductor version 3.22 (BiocManager 1.30.27), R 4.5.2 (2025-10-31)
Installing package(s) 'hgu133a.db'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES':
  status was 'SSL connect error'
unable to access index for repository
  https://bioconductor.org/packages/3.22/data/experiment/src/contrib: cannot
  open URL
  'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
URL
  'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/workflows/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES.rds':
  status was 'SSL connect error'
URL 'https://bioconductor.org/packages/3.22/books/src/contrib/PACKAGES.gz':
  status was 'SSL connect error'
trying URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133a.db_3.13.0.tar.gz'
URL
  'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133a.db_3.13.0.tar.gz':
  status was 'SSL connect error'
Error in download.file(urls, destfiles, "libcurl", mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133a.db_3.13.0.tar.gz'
download of package ‘hgu133a.db’ failed
Corresponding annotation package not found: hgu133plus2.db
Make sure that you have it installed.
URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
cannot open URL 'https://bioconductor.org/config.yaml'
URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
cannot open URL 'http://bioconductor.org/config.yaml'
Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
Bioconductor version 3.22 (BiocManager 1.30.27), R 4.5.2 (2025-10-31)
Installing package(s) 'hgu133plus2.db'
trying URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133plus2.db_3.13.0.tar.gz'
Content type 'application/x-gzip' length 2240377 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

* installing *source* package ‘hgu133plus2.db’ ...
** this is package ‘hgu133plus2.db’ version ‘3.13.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (hgu133plus2.db)

The downloaded source packages are in
	‘/tmp/RtmpjynA4Y/downloaded_packages’
Error in get(anno.pkg) : object 'hgu133a.db' not found
Calls: maPreproc ... withCallingHandlers -> sapply -> lapply -> FUN -> get
Execution halted
* 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-3.22-bioc/meat/GSEABenchmarkeR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GSEABenchmarkeR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GSEABenchmarkeR’ ...
** this is package ‘GSEABenchmarkeR’ version ‘1.30.0’
** 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 (GSEABenchmarkeR)