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BioC 2.13: CHECK report for virtualArray on zin1

This page was generated on 2013-10-20 09:46:32 -0700 (Sun, 20 Oct 2013).

Package 735/749HostnameOS / ArchBUILDCHECKBUILD BIN
virtualArray 1.6.0
Andreas Heider
Snapshot Date: 2013-10-19 16:20:26 -0700 (Sat, 19 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/virtualArray
Last Changed Rev: 81642 / Revision: 81880
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.2 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: virtualArray
Version: 1.6.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings virtualArray_1.6.0.tar.gz
StartedAt: 2013-10-20 03:15:11 -0700 (Sun, 20 Oct 2013)
EndedAt: 2013-10-20 03:17:34 -0700 (Sun, 20 Oct 2013)
EllapsedTime: 142.7 seconds
RetCode: 0
Status:  OK 
CheckDir: virtualArray.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/virtualArray.Rcheck’
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘virtualArray/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘virtualArray’ version ‘1.6.0’
* package encoding: latin1
* 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 ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘plyr’ ‘preprocessCore’
  These packages needs to imported from for the case when
  this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘virtualArray/R/onLoad.R’:
  .onLoad calls:
    message("To support our work please cite:")
    print(citation("virtualArray"))
    message("Thanks.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

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 ... [19s/20s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
virtualArrayBuildfData 5.621   0.16   5.797
virtualArrayBuildExprs 4.500   0.14   5.146
* 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

NOTE: There were 6 notes.
See
  ‘/home/biocbuild/bbs-2.13-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 ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
Creating a generic function from function ‘virtualArrayComBat’ in package ‘virtualArray’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘affyPLM’
Warning: replacing previous import by ‘methods::new’ when loading ‘virtualArray’
Warning: replacing previous import by ‘stats::density’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::installed.packages’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.csv’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::read.table’ when loading ‘virtualArray’
Warning: replacing previous import by ‘utils::write.table’ when loading ‘virtualArray’
To support our work please cite:

To cite package 'virtualArray' in publications use:

  Andreas Heider and Rüdiger Alt (2013). virtualArray: a R/bioconductor
  package to merge raw data from different microarray platforms. R
  package version 1.6.0.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {virtualArray: a R/bioconductor package to merge raw data from different microarray platforms},
    author = {{Andreas Heider} and {Rüdiger Alt}},
    year = {2013},
    note = {R package version 1.6.0},
    journal = {BMC Bioinformatics},
    volume = {14},
    pages = {75},
  }

Thanks.
* DONE (virtualArray)

virtualArray.Rcheck/virtualArray-Ex.timings:

nameusersystemelapsed
GPLs0.0040.0000.004
normalize.ExpressionSet.gq0.1680.0040.177
normalize.ExpressionSet.mc0.0000.0000.002
normalize.ExpressionSet.mrs0.0040.0000.004
normalize.ExpressionSet.nordi0.0000.0000.002
normalize.ExpressionSet.qd0.0040.0000.003
sample_info_imported0.0080.0000.008
virtualArray-package0.0040.0000.003
virtualArrayBuildExprs4.5000.1405.146
virtualArrayBuildSampleInfo2.7080.0362.779
virtualArrayBuildfData5.6210.1605.797
virtualArrayComBat0.0080.0000.007
virtualArrayCompile0.0080.0000.007
virtualArrayDirs0.0040.0000.004
virtualArrayExpressionSets0.0040.0000.001
virtualArrayHclust0.0160.0000.015
virtualArrayLoadRaw000
virtualArrayMergeRecurse0.0160.0000.019