##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:curatedCRCData.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings curatedCRCData_2.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedCRCData.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘curatedCRCData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedCRCData’ version ‘2.41.1’
* 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 ‘curatedCRCData’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 399.2Mb
  sub-directories of 1Mb or more:
    data  398.9Mb
* 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
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 ‘curatedCRCData_vignette.Rnw’ using Sweave
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-3. For overview type 'help("mgcv-package")'.
Loading required package: genefilter
Loading required package: BiocParallel

Error: processing vignette 'curatedCRCData_vignette.Rnw' failed with diagnostics:
 chunk 2 (label = preliminaries) 
Error in library(affy) : there is no package called ‘affy’

--- failed re-building ‘curatedCRCData_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘curatedCRCData_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/curatedCRCData.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL curatedCRCData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘curatedCRCData’ ...
** this is package ‘curatedCRCData’ version ‘2.41.1’
** using staged installation
** R
** data
** 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
Warning in fun(libname, pkgname) :
  Package 'curatedCRCData' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'curatedCRCData' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (curatedCRCData)