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BioC 3.2: CHECK report for MmPalateMiRNA on linux1.bioconductor.org

This page was generated on 2015-10-27 17:25:16 -0400 (Tue, 27 Oct 2015).

Package 663/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MmPalateMiRNA 1.20.0
Guy Brock
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MmPalateMiRNA
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MmPalateMiRNA
Version: 1.20.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MmPalateMiRNA_1.20.0.tar.gz
StartedAt: 2015-10-27 05:54:24 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:55:10 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 45.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MmPalateMiRNA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MmPalateMiRNA_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MmPalateMiRNA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.20.0’
* 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 : .local : <anonymous>: no visible global function
  definition for ‘RG.MA’
MADvsMedianPlot,list : .local : <anonymous>: no visible global function
  definition for ‘assayData’
MADvsMedianPlot,list : .local : <anonymous>: no visible global function
  definition for ‘pData’
MADvsMedianPlot,list : .local : <anonymous>: no visible global function
  definition for ‘featureData’
MAplot,NChannelSet: no visible global function definition for
  ‘assayData’
densityplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘RG.MA’
densityplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘assayData’
densityplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘pData’
densityplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘featureData’
levelplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘RG.MA’
levelplot,list-missing : .local : <anonymous>: no visible global
  function definition for ‘assayData’
* 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 ... [9s/9s] 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-3.2-bioc/meat/MmPalateMiRNA.Rcheck/00check.log’
for details.


MmPalateMiRNA.Rcheck/00install.out:

* 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)

MmPalateMiRNA.Rcheck/MmPalateMiRNA-Ex.timings:

nameusersystemelapsed
MADvsMedianPlot1.3570.0121.371
MAplot0.5860.0040.592
PalateData0.0790.0000.079
checkMVs0.3020.0000.302
checkOutliers1.2300.0081.238
clustPlot0.0660.0000.066
densityplot0.9700.0000.971
filterArray0.1260.0040.130
fixMVs0.3220.0000.324
fixOutliers1.2330.0041.237
imputeKNN0.0080.0000.007
levelplot0.7380.0000.738