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Package 645/658HostnameOS / ArchBUILDCHECKBUILD BIN
virtualArray 1.3.1
Andreas Heider
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/virtualArray
Last Changed Rev: 72530 / Revision: 74756
Last Changed Date: 2013-01-15 00:19:09 -0800 (Tue, 15 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: virtualArray
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch virtualArray_1.3.1.tar.gz
StartedAt: 2013-03-24 11:01:13 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 11:05:03 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 230.5 seconds
RetCode: 0
Status:  OK 
CheckDir: virtualArray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/virtualArray.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'virtualArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'virtualArray' version '1.3.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'multicore'
* 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 'virtualArray' can be installed ... [20s/21s] OK
* checking installed package size ... OK
* checking package 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 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
nordi1p_getoutliers: no visible global function definition for
  'rm.outlier'
virtualArrayBuildfData: no visible global function definition for
  'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
  'biocinstallRepos'
virtualArrayExpressionSets: no visible global function definition for
  'register'
virtualArrayExpressionSets: no visible global function definition for
  'MulticoreParam'
virtualArrayExpressionSets: no visible binding for global variable
  'bplapply'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U133Plus2'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U219'
virtualArrayLoadRaw: no visible binding for global variable
  'rawdata_U133A'
virtualArrayComBat,data.frame: no visible global function definition
  for 'as.data.matrix'
* checking Rd files ... NOTE
prepare_Rd: normalize.ExpressionSet.gq.Rd:41-43: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mc.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.mrs.Rd:40-42: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.nordi.Rd:42-44: Dropping empty section \note
prepare_Rd: normalize.ExpressionSet.qd.Rd:39-41: Dropping empty section \note
* 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' ... NOTE
The following files should probably not be installed:
  'virtualArray-016.pdf'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [30s/33s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
virtualArrayBuildfData 8.477  0.457  11.290
virtualArrayBuildExprs 7.290  0.189   7.498
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/virtualArray.Rcheck/00check.log'
for details.

virtualArray.Rcheck/00install.out:

* installing *source* package 'virtualArray' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
Creating a generic function from function 'virtualArrayComBat' in package 'virtualArray'
** help
*** installing help indices
** building package indices
** installing vignettes
   'virtualArray.Rnw' 
** testing if installed package can be loaded
Creating a generic function for 'boxplot' from package 'graphics' in package 'affyPLM'
Creating a generic function for 'hist' from package 'graphics' in package 'affyPLM'
Warning: replacing previous import 'new' when loading 'methods'
* DONE (virtualArray)

virtualArray.Rcheck/virtualArray-Ex.timings:

nameusersystemelapsed
GPLs0.0050.0030.009
normalize.ExpressionSet.gq0.0050.0010.006
normalize.ExpressionSet.mc0.0050.0020.007
normalize.ExpressionSet.mrs0.0070.0020.009
normalize.ExpressionSet.nordi0.0110.0040.015
normalize.ExpressionSet.qd0.0090.0020.011
sample_info_imported0.0140.0030.016
virtualArray-package0.0080.0020.011
virtualArrayBuildExprs7.2900.1897.498
virtualArrayBuildSampleInfo3.9740.1844.158
virtualArrayBuildfData 8.477 0.45711.290
virtualArrayComBat0.0160.0080.025
virtualArrayCompile0.0030.0060.010
virtualArrayDirs0.0050.0100.015
virtualArrayExpressionSets0.0160.0060.022
virtualArrayHclust0.0280.0130.041
virtualArrayLoadRaw0.0030.0040.006
virtualArrayMergeRecurse0.0340.0150.048