Package: MmPalateMiRNA

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MmPalateMiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MmPalateMiRNA_1.34.0.tar.gz

StartedAt: 2019-10-16 05:19:35 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:20:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MmPalateMiRNA.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MmPalateMiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MmPalateMiRNA_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MmPalateMiRNA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MmPalateMiRNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MmPalateMiRNA' version '1.34.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'xtable', 'limma', 'statmod', 'lattice', 'vsn'
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 whether package 'MmPalateMiRNA' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:36: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:40: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:49: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:50: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MAplot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MAplot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:29: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:33: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:34: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:35: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:36: file link 'lattice-package' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:9: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:22: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:8: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:23: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:32: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:33: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:34: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:40: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:44: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:51: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:60: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:61: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/filterArray.Rd:8: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/filterArray.Rd:12: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/filterArray.Rd:26: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/filterArray.Rd:57: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:37: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:38: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:39: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:45: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:59: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:68: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:69: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MmPalateMiRNA.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'limma' 'lattice' 'Biobase'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
  'methods' 'statmod' 'vsn' 'xtable'
  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
clustPlot: no visible global function definition for 'par'
clustPlot: no visible global function definition for 'plot'
clustPlot: no visible global function definition for 'axis'
clustPlot: no visible global function definition for 'lines'
clustPlot: no visible global function definition for 'legend'
fixOutliers : : no visible global function definition for
  'sd'
imputeKNN: no visible global function definition for 'sd'
imputeKNN: no visible global function definition for 'cor'
MADvsMedianPlot,list : : no visible global function
  definition for 'RG.MA'
MADvsMedianPlot,list : : no visible global function
  definition for 'assayData'
MADvsMedianPlot,list : : no visible binding for global
  variable 'mad'
MADvsMedianPlot,list : : no visible binding for global
  variable 'median'
MADvsMedianPlot,list: no visible global function definition for 'stack'
MADvsMedianPlot,list : : no visible global function
  definition for 'pData'
MADvsMedianPlot,list : : no visible global function
  definition for 'featureData'
MAplot,MAList: no visible global function definition for 'stack'
MAplot,NChannelSet: no visible global function definition for
  'assayData'
MAplot,NChannelSet: no visible global function definition for 'stack'
checkOutliers,RGList: no visible binding for global variable 'sd'
densityplot,RGList-missing: no visible global function definition for
  'as.formula'
densityplot,list-missing : : no visible global function
  definition for 'RG.MA'
densityplot,list-missing : : no visible global function
  definition for 'assayData'
densityplot,list-missing : : no visible global function
  definition for 'pData'
densityplot,list-missing : : no visible global function
  definition for 'featureData'
densityplot,list-missing: no visible global function definition for
  'as.formula'
levelplot,RGList-missing: no visible global function definition for
  'median'
levelplot,list-missing : : no visible global function
  definition for 'RG.MA'
levelplot,list-missing : : no visible global function
  definition for 'assayData'
levelplot,list-missing: no visible global function definition for
  'median'
Undefined global functions or variables:
  RG.MA as.formula assayData axis cor featureData legend lines mad
  median pData par plot sd stack
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "cor", "mad", "median", "sd")
  importFrom("utils", "stack")
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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/MmPalateMiRNA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MmPalateMiRNA_1.34.0.tar.gz && rm -rf MmPalateMiRNA.buildbin-libdir && mkdir MmPalateMiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MmPalateMiRNA.buildbin-libdir MmPalateMiRNA_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MmPalateMiRNA_1.34.0.zip && rm MmPalateMiRNA_1.34.0.tar.gz MmPalateMiRNA_1.34.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  506k  100  506k    0     0  4836k      0 --:--:-- --:--:-- --:--:-- 5226k

install for i386

* installing *source* package 'MmPalateMiRNA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MmPalateMiRNA'
    finding HTML links ... done
    MADvsMedianPlot                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:36: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:40: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:49: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MADvsMedianPlot.Rd:50: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    MAplot                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MAplot.Rd:29: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MAplot.Rd:30: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
    MmPalateMiRNA-package                   html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:29: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:33: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:34: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:35: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/MmPalateMiRNA-package.Rd:36: file link 'lattice-package' in package 'lattice' does not exist and so has been treated as a topic
    PalateData                              html  
    finding level-2 HTML links ... done

    checkMVs                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:9: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkMVs.Rd:22: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
    checkOutliers                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:8: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:13: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/checkOutliers.Rd:23: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
    clustPlot                               html  
    densityplot                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:32: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:33: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:34: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:40: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:44: file link 'densityplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:51: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/densityplot.Rd:60: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
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    filterArray                             html  
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    fixMVs                                  html  
    fixOutliers                             html  
    imputeKNN                               html  
    levelplot                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:37: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:38: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:39: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:45: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:59: file link 'RGList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:68: file link 'MAList-class' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi89bk6/R.INSTALL59c70ff3e8e/MmPalateMiRNA/man/levelplot.Rd:69: file link 'NChannelSet-class' in package 'Biobase' does not exist and so has been treated as a topic
** 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

install for x64

* installing *source* package 'MmPalateMiRNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MmPalateMiRNA' as MmPalateMiRNA_1.34.0.zip
* DONE (MmPalateMiRNA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MmPalateMiRNA' successfully unpacked and MD5 sums checked