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Package 2/479HostnameOS / ArchBUILDCHECKBUILD BIN
a4Base 1.1.3
Tobias Verbeke
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4Base
Last Changed Rev: 55770 / Revision: 56603
Last Changed Date: 2011-05-21 07:15:35 -0700 (Sat, 21 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  ERROR 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: a4Base
Version: 1.1.3
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.1.3.tar.gz
StartedAt: 2011-07-07 01:01:06 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:07:58 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 411.5 seconds
RetCode: 0
Status:  OK 
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/a4Base.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.1.3'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'gridSVG' 'JavaGD'
* checking if this is a source package ... OK
* checking whether package 'a4Base' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for
  'grid.hyperlink'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
* 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 ... NOTE
'library' or 'require' call not declared from: 'nlcv'
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

a4Base.Rcheck/00install.out:

* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: DBI

Loading required package: KEGG.db

Loading required package: MASS
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-17


Attaching package: 'genefilter'

The following object(s) are masked from 'package:MASS':

    area

Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loaded glmnet 1.7 

Attaching package: 'a4Core'

The following object(s) are masked from 'package:limma':

    topTable

Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object(s) are masked from 'package:Biobase':

    combine

The following object(s) are masked from 'package:stats':

    nobs

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: caTools
Loading required package: bitops

Attaching package: 'gplots'

The following object(s) are masked from 'package:multtest':

    wapply

The following object(s) are masked from 'package:stats':

    lowess

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

mpm version 1.0-17

Loaded glmnet 1.7 

a4Base version 1.1.3


* DONE (a4Base)

a4Base.Rcheck/a4Base-Ex.timings:

nameusersystemelapsed
a4palette0.0220.0000.023
addQuantilesColors4.7280.3325.304
boxPlot5.6980.3166.102
combineTwoExpressionSet0.0000.0000.001
computeLogRatio22.193 0.63324.092
createExpressionSet0.1040.0010.114
filterVarInt5.5180.2236.284
heatmap.expressionSet0.0020.0010.002
histPvalue5.5500.3276.168
histpvalueplotter5.5330.3425.975
lassoReg5.0940.2875.477
logReg5.0140.2755.453
nlcvTT3.6680.0973.831
plot1gene4.9710.2885.371
plotComb2Samples5.1620.3035.569
plotCombMultSamples5.4200.4116.187
plotCombination2genes4.9990.2785.331
plotLogRatio22.754 0.63523.901
probabilitiesPlot5.1060.3055.531
probe2gene5.1700.2145.412
profilesPlot5.0520.2785.395
propdegenescalculation5.5930.3756.118
replicates0.0030.0000.005
spectralMap31.259 5.71738.679
tTest5.5930.4766.153
volcanoPlot5.7670.4726.602