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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Hiiragi2013.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Hiiragi2013_1.45.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/Hiiragi2013.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 ‘Hiiragi2013/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Hiiragi2013’ version ‘1.45.3’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'KEGGREST', 'affy', 'boot', 'clue', 'genefilter', 'geneplotter',
  'gtools', 'mouse4302.db', 'xtable'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘Hiiragi2013’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘boot::logit’ by ‘gtools::logit’ when loading ‘Hiiragi2013’
  Warning: replacing previous import ‘boot::inv.logit’ by ‘gtools::inv.logit’ when loading ‘Hiiragi2013’
See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/Hiiragi2013.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
  installed size is 136.5Mb
  sub-directories of 1Mb or more:
    data  136.3Mb
* 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 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'MDSplot.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'getDifferentialExpressedGenes.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'myHeatmap.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'myHeatmap2.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'pamCluster.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'x.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'xq.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'xql.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
a 25.038  1.715  27.604
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/Hiiragi2013.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Hiiragi2013
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Hiiragi2013’ ...
** this is package ‘Hiiragi2013’ version ‘1.45.3’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘boot::logit’ by ‘gtools::logit’ when loading ‘Hiiragi2013’
Warning: replacing previous import ‘boot::inv.logit’ by ‘gtools::inv.logit’ when loading ‘Hiiragi2013’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘boot::logit’ by ‘gtools::logit’ when loading ‘Hiiragi2013’
Warning: replacing previous import ‘boot::inv.logit’ by ‘gtools::inv.logit’ when loading ‘Hiiragi2013’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘boot::logit’ by ‘gtools::logit’ when loading ‘Hiiragi2013’
Warning: replacing previous import ‘boot::inv.logit’ by ‘gtools::inv.logit’ when loading ‘Hiiragi2013’
** testing if installed package keeps a record of temporary installation path
* DONE (Hiiragi2013)