##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:curatedCRCData.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings curatedCRCData_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-data-experiment/meat/curatedCRCData.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘curatedCRCData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘curatedCRCData’ version ‘2.32.0’
* 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 ‘curatedCRCData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 399.7Mb
  sub-directories of 1Mb or more:
    data  399.4Mb
* 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 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘curatedCRCData_vignette.Rnw’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘curatedCRCData_vignette.Rnw’
  ...
Loading required package: genefilter
Loading required package: BiocParallel

> library(xtable)

> library(affy)

  When sourcing ‘curatedCRCData_vignette.R’:
Error: there is no package called ‘affy’
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘curatedCRCData_vignette.Rnw’ using Sweave
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.9-0. 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-data-experiment/meat/curatedCRCData.Rcheck/00check.log’
for details.