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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:categoryCompare.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings categoryCompare_1.54.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/categoryCompare.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 ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.54.0’
* 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 ‘categoryCompare’ 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 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
.ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOTERM’
.ccCompareGO: no visible binding for global variable ‘Term’
.cytOutNodes: ... may be used in an incorrect context:
  exportImage(filename = fileName, type = "png", network = cwObj, ...)
.getDesc : <anonymous>: no visible global function definition for
  ‘Term’
show,HyperGResultCC: no visible global function definition for
  ‘description’
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM Term description
* checking Rd files ... NOTE
checkRd: (-1) ccData.Rd:21: Lost braces
    21 |   \code{table10}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 10 hours}
       |                 ^
checkRd: (-1) ccData.Rd:23: Lost braces
    23 |   \code{table48}{: Log-ratio output from \pkg{limma} for the comparison of presence-absence of estrogen at 48 hours}
       |                 ^
checkRd: (-1) ccData.Rd:25: Lost braces
    25 |   \code{gUniverse}{: All of the genes measured on the chip}
       |                   ^
checkRd: (-1) ccData.Rd:27: Lost braces
    27 |         \code{gseaRes}{: Toy results of GSEA analysis of 3 different tissues}
       |                       ^
checkRd: (-1) ccData.Rd:29: Lost braces
    29 |         \code{enrichLists}{: Apply \code{\link{ccEnrich}} to a ccGeneList from \code{table10} and \code{table48}}
       |                           ^
checkRd: (-1) ccData.Rd:31: Lost braces
    31 |         \code{ccResults}{: Apply \code{\link{ccCompare}} to \code{enrichLists}}
       |                         ^
checkRd: (-1) ccData.Rd:33: Lost braces
    33 |         \code{ccResultsBPHier}{: Modify \code{enrichLists$BP} to use a "hierarchical" layout}
       |                               ^
checkRd: (-1) ccData.Rd:35: Lost braces
    35 |         \code{geneLists}{: a \code{ccGeneList} generated from genes in table10 and table48}
       |                         ^
checkRd: (-1) ccData.Rd:37: Lost braces
    37 |         \code{ccOpts}{: a \code{ccOptions} object describing what we are going to do as far as feature list comparisons}
       |                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GENccEnrichResult-class.Rd: AssayData-class
  HyperGResultCC-class.Rd: HyperGParams-class, HyperGResult-class,
    HyperGResultBase-class
  ccCompareCollection-class.Rd: AssayData-class
  ccEnrichCollection-class.Rd: AssayData-class
  ccEnrichResult-class.Rd: AssayData-class
  mergedData-class.Rd: data.frameOrNULL-class
  resetColors-methods.Rd: setNodeColorMapping
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘categoryCompare_vignette.Rmd’ using rmarkdown

Quitting from categoryCompare_vignette.Rmd:45-47 [normalizeAffy]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
---
Backtrace:
     ▆
  1. └─affy::mas5(a)
  2.   └─affy::expresso(...)
  3.     ├─base::do.call(...)
  4.     ├─affy::bg.correct(afbatch, method = bgcorrect.method)
  5.     └─affy::bg.correct(afbatch, method = bgcorrect.method)
  6.       ├─base::do.call(methodname, alist(object, ...))
  7.       └─affy::bg.correct.mas(object, ...)
  8.         ├─base::unique(unlist(indexProbes(object, "pm")))
  9.         ├─base::unlist(indexProbes(object, "pm"))
 10.         ├─affy::indexProbes(object, "pm")
 11.         └─affy::indexProbes(object, "pm")
 12.           └─affy (local) .local(object, which, ...)
 13.             └─affy::getCdfInfo(object)
 14.               └─affy::cdfFromBioC(cdfname, cur$where, verbose)
 15.                 ├─base::sapply(repositories(), contrib.url)
 16.                 │ └─base::lapply(X = X, FUN = FUN, ...)
 17.                 └─BiocManager::repositories()
 18.                   └─BiocManager:::.version_validate(version)
 19.                     ├─base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
 20.                     └─BiocManager:::.stop(txt)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'categoryCompare_vignette.Rmd' failed with diagnostics:
Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
--- failed re-building ‘categoryCompare_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘categoryCompare_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL categoryCompare
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘categoryCompare’ ...
** this is package ‘categoryCompare’ version ‘1.54.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: ... may be used in an incorrect context 
** 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 (categoryCompare)