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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gaia.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gaia_2.39.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/gaia.Rcheck'
* using R Under development (unstable) (2022-02-17 r81757 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gaia/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gaia' version '2.39.0'
* 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 whether package 'gaia' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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
generate_approx_null_hypothesis: no visible global function definition
  for 'rbinom'
qvalue: no visible global function definition for 'smooth.spline'
qvalue: no visible global function definition for 'predict'
runGAIA: no visible global function definition for 'write.table'
write_significant_regions: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  predict rbinom smooth.spline write.table
Consider adding
  importFrom("stats", "predict", "rbinom", "smooth.spline")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
runGAIA 5.26   0.15    5.42
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/gaia.Rcheck/00check.log'
for details.

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###
### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gaia
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'gaia' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gaia'
    finding HTML links ... done
    crc                                     html  
    crc_markers                             html  
    gaia-package                            html  
    generate_approx_null_hypothesis         html  
    generate_null_hypothesis                html  
    load_cnv                                html  
    load_markers                            html  
    peel_off                                html  
    qvalue                                  html  
    runGAIA                                 html  
    search_peaks_in_regions                 html  
    synthCNV_Matrix                         html  
    synthMarkers_Matrix                     html  
    write_significant_regions               html  
** 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 (gaia)
Making 'packages.html' ... done