BioC 3.3: CHECK report for MmPalateMiRNA on linux2.bioconductor.org

Package: MmPalateMiRNA

Version: 1.21.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MmPalateMiRNA_1.21.0.tar.gz

StartedAt: 2015-10-27 05:58:38 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:59:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 47.4 seconds

RetCode: 0

Status:  OK

CheckDir: MmPalateMiRNA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MmPalateMiRNA_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MmPalateMiRNA.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MmPalateMiRNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MmPalateMiRNA’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MmPalateMiRNA’ can be installed ... [4s/4s] OK
* 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
* 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 ... 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
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘RG.MA’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘assayData’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘pData’
MADvsMedianPlot,list : <anonymous>: no visible global function
  definition for ‘featureData’
MAplot,NChannelSet: no visible global function definition for
  ‘assayData’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘RG.MA’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘assayData’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘pData’
densityplot,list-missing : <anonymous>: no visible global function
  definition for ‘featureData’
levelplot,list-missing : <anonymous>: no visible global function
  definition for ‘RG.MA’
levelplot,list-missing : <anonymous>: no visible global function
  definition for ‘assayData’
Undefined global functions or variables:
  RG.MA assayData featureData pData
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/MmPalateMiRNA.Rcheck/00check.log’
for details.

* installing *source* package ‘MmPalateMiRNA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MmPalateMiRNA)

name	user	system	elapsed
MADvsMedianPlot	1.324	0.015	1.347
MAplot	0.597	0.008	0.612
PalateData	0.091	0.004	0.096
checkMVs	0.236	0.000	0.237
checkOutliers	1.262	0.008	1.277
clustPlot	0.073	0.000	0.074
densityplot	0.849	0.012	0.861
filterArray	0.086	0.000	0.087
fixMVs	0.322	0.004	0.327
fixOutliers	1.244	0.000	1.245
imputeKNN	0.007	0.000	0.008
levelplot	0.532	0.008	0.541