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BioC 3.2: CHECK report for MmPalateMiRNA on moscato1

This page was generated on 2016-04-23 10:18:09 -0700 (Sat, 23 Apr 2016).

Package 663/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MmPalateMiRNA 1.20.0
Guy Brock
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MmPalateMiRNA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: rm -rf MmPalateMiRNA.buildbin-libdir MmPalateMiRNA.Rcheck && mkdir MmPalateMiRNA.buildbin-libdir MmPalateMiRNA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MmPalateMiRNA.buildbin-libdir MmPalateMiRNA_1.20.0.tar.gz >MmPalateMiRNA.Rcheck\00install.out 2>&1 && cp MmPalateMiRNA.Rcheck\00install.out MmPalateMiRNA-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MmPalateMiRNA.buildbin-libdir --install="check:MmPalateMiRNA-install.out" --force-multiarch --no-vignettes --timings MmPalateMiRNA_1.20.0.tar.gz
StartedAt: 2016-04-23 04:54:53 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:56:43 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 110.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MmPalateMiRNA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf MmPalateMiRNA.buildbin-libdir MmPalateMiRNA.Rcheck && mkdir MmPalateMiRNA.buildbin-libdir MmPalateMiRNA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MmPalateMiRNA.buildbin-libdir MmPalateMiRNA_1.20.0.tar.gz >MmPalateMiRNA.Rcheck\00install.out 2>&1 && cp MmPalateMiRNA.Rcheck\00install.out MmPalateMiRNA-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MmPalateMiRNA.buildbin-libdir --install="check:MmPalateMiRNA-install.out" --force-multiarch --no-vignettes --timings MmPalateMiRNA_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MmPalateMiRNA.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.20.0'
* 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 whether package 'MmPalateMiRNA' can be installed ... 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
* 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
** checking loading without being on the library search path ... 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 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 ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [10s] 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
  'D:/biocbld/bbs-3.2-bioc/meat/MmPalateMiRNA.Rcheck/00check.log'
for details.


MmPalateMiRNA.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'MmPalateMiRNA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MmPalateMiRNA' as MmPalateMiRNA_1.20.0.zip
* DONE (MmPalateMiRNA)

MmPalateMiRNA.Rcheck/examples_i386/MmPalateMiRNA-Ex.timings:

nameusersystemelapsed
MADvsMedianPlot1.630.021.65
MAplot0.680.000.67
PalateData0.080.000.08
checkMVs0.190.000.19
checkOutliers1.540.011.56
clustPlot0.090.020.10
densityplot1.350.001.36
filterArray0.170.020.19
fixMVs0.180.000.19
fixOutliers1.240.011.24
imputeKNN000
levelplot0.540.020.57

MmPalateMiRNA.Rcheck/examples_x64/MmPalateMiRNA-Ex.timings:

nameusersystemelapsed
MADvsMedianPlot1.440.031.47
MAplot0.590.010.61
PalateData0.080.000.07
checkMVs0.160.040.19
checkOutliers1.260.011.28
clustPlot0.080.000.08
densityplot1.280.021.29
filterArray0.110.000.11
fixMVs0.320.000.33
fixOutliers1.160.001.15
imputeKNN0.010.000.02
levelplot0.940.000.93