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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFEA.ChIP.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings TFEA.ChIP_1.29.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/TFEA.ChIP.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TFEA.ChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TFEA.ChIP' version '1.29.2'
* 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 whether package 'TFEA.ChIP' can be installed ... OK
* checking installed package size ... INFO
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   9.2Mb
    doc    1.9Mb
* checking package directory ... OK
* checking 'build' directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
  'inst/doc/TFEA.ChIP.html'
Source(s) listed in 'build/vignette.rds' but not in package:
  'TFEA.ChIP.Rmd'
R code(s) listed in 'build/vignette.rds' but not in package:
  'TFEA.ChIP.R'
* 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 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 ... 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' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'CMplot1.png' 'CMplot2.png' 'GSEAplot1.png' 'GSEAplot2.png'
  'TFEA.ChIP.Rmd' 'meta_hif1a.png' 'meta_table.png' 'rankTFplot.png'
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
rankTFs             18.87   0.76   19.65
GSEA_run            15.39   1.19   16.83
analysis_from_table  6.22   0.52    6.75
getCMstats           5.81   0.33    6.14
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignette without corresponding single PDF/HTML:
  'TFEA.ChIP.Rmd'
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/TFEA.ChIP.Rcheck/00check.log'
for details.