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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CINdex.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CINdex_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CINdex.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘CINdex/DESCRIPTION’ ... OK
* this is package ‘CINdex’ version ‘1.38.0’
* 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 ‘CINdex’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data  16.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
comp.heatmap: no visible binding for global variable ‘dataMatrix’
process.probe.anno: no visible binding for global variable ‘ID’
process.probe.anno: no visible binding for global variable ‘midpoint’
process.reference.genome: no visible binding for global variable
  ‘chrom’
process.reference.genome: no visible binding for global variable ‘name’
process.reference.genome: no visible binding for global variable
  ‘stain’
run.cin.chr: no visible global function definition for ‘is’
run.cin.cyto: no visible global function definition for ‘is’
Undefined global functions or variables:
  ID chrom dataMatrix is midpoint name stain
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... WARNING
  LazyData DB of 16.5 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
run.cin.cyto 10.013   0.44  10.454
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘RunTests.R’
 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 ‘HowToDownloadCytobandInfo.Rmd’ using rmarkdown
--- finished re-building ‘HowToDownloadCytobandInfo.Rmd’

--- re-building ‘PrepareInputData.Rmd’ using rmarkdown

Quitting from PrepareInputData.Rmd:289-309 [GeneAnn]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.updateTxDb()`:
! Could not load package txdbmaker. Is it installed?

  Note that the TxDb() method for OrganismDb objects requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
---
Backtrace:
    x
 1. +-OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`)
 2. \-OrganismDbi::`TxDb<-`(`*tmp*`, value = `<TxDb>`)
 3.   \-OrganismDbi:::.updateTxDb(x, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'PrepareInputData.Rmd' failed with diagnostics:
Could not load package txdbmaker. Is it installed?

  Note that the TxDb() method for OrganismDb objects requires the txdbmaker
  package. Please install it with:

    BiocManager::install("txdbmaker")
--- failed re-building ‘PrepareInputData.Rmd’

--- re-building ‘CINdex.Rnw’ using knitr
--- finished re-building ‘CINdex.Rnw’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CINdex.Rcheck/00check.log’
for details.