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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeconRNASeq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeconRNASeq_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DeconRNASeq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DeconRNASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DeconRNASeq’ version ‘1.49.0’
* 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 ‘DeconRNASeq’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘grid’ ‘pcaMethods’
  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
DeconRNASeq: no visible global function definition for ‘prep’
DeconRNASeq: no visible global function definition for ‘pca’
DeconRNASeq: no visible global function definition for ‘R2cum’
DeconRNASeq: no visible global function definition for ‘ggplot’
DeconRNASeq: no visible global function definition for ‘aes’
DeconRNASeq: no visible global function definition for ‘geom_point’
DeconRNASeq: no visible global function definition for ‘labs’
DeconRNASeq: no visible global function definition for ‘geom_abline’
DeconRNASeq: no visible global function definition for ‘xlab’
DeconRNASeq: no visible global function definition for ‘ylab’
condplot: no visible global function definition for ‘rainbow’
condplot: no visible global function definition for ‘lines’
condplot: no visible global function definition for ‘axis’
condplot: no visible global function definition for ‘title’
decon.bootstrap: no visible global function definition for ‘t.test’
multiplot: no visible global function definition for ‘grid.newpage’
multiplot: no visible global function definition for ‘pushViewport’
multiplot: no visible global function definition for ‘viewport’
multiplot: no visible global function definition for ‘grid.layout’
multiplot : vplayout: no visible global function definition for
  ‘viewport’
Undefined global functions or variables:
  R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage
  labs lines pca prep pushViewport rainbow t.test title viewport xlab
  ylab
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "lines", "title")
  importFrom("stats", "t.test")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DeconRNASeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeconRNASeq
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DeconRNASeq’ ...
** using staged installation
** R
** data
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (DeconRNASeq)