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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:yri1kgv.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings yri1kgv_0.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/yri1kgv.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘yri1kgv/DESCRIPTION’ ... OK
* this is package ‘yri1kgv’ version ‘0.32.0’
* 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 ‘yri1kgv’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.12-data-experiment/meat/yri1kgv.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 323.9Mb
  sub-directories of 1Mb or more:
    data    17.4Mb
    parts  305.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Package in Depends field not imported from: ‘GGBase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘yri1kgv/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste("To get a tailored smlSet, use getSS(\"",     pkgname, "\", [chrvec])", sep = ""), "\n")
    packageStartupMessage("available chromosomes are named ", paste(selectSome(cn),     collapse = ", "), "\n")

See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... NOTE
prepare_Rd: yri1kgv-package.Rd:41-44: Dropping empty section \seealso
prepare_Rd: yri1kgv-package.Rd:45-46: Dropping empty section \examples
* 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 examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-data-experiment/meat/yri1kgv.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL yri1kgv
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘yri1kgv’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13 
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'GGBase' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (yri1kgv)