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BioC 2.13: CHECK report for ArrayTools on perceval

This page was generated on 2014-04-05 09:52:10 -0700 (Sat, 05 Apr 2014).

Package 52/750HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayTools 1.22.0
Arthur Li
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ArrayTools
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 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 [ OK ] OK 

Summary

Package: ArrayTools
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayTools_1.22.0.tar.gz
StartedAt: 2014-04-04 23:30:18 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:32:19 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 121.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ArrayTools’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘ArrayTools’ can be installed ... [8s/8s] 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:
  ‘affy’ ‘Biobase’ ‘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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
preProcessGeneST: no visible binding for global variable
  ‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
  ‘mogene10stCONTROL’
regress: no visible global function definition for ‘permute.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘ArrayTools.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
preProcess3prime 7.81  0.156   7.979
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ArrayTools.Rcheck/00check.log’
for details.

ArrayTools.Rcheck/00install.out:

* installing *source* package ‘ArrayTools’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ArrayTools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ArrayTools)

ArrayTools.Rcheck/ArrayTools-Ex.timings:

nameusersystemelapsed
Output2HTML0.1740.0090.183
QC0.0070.0010.007
Sort0.2130.0060.219
contrastMatrix-class0.0690.0030.072
createExpressionSet0.1010.0010.102
createGSEAFiles0.0080.0000.009
createIndex0.3460.0050.351
createIngenuityFile0.0920.0010.093
designMatrix-class0.0290.0010.031
eSetExample0.0080.0010.009
exprsExample0.0090.0010.010
geneFilter4.2690.0864.355
interactionResult-class0.8710.0240.895
pDataExample0.0110.0010.013
postInteraction0.3010.0050.307
preProcess3prime7.8100.1567.979
preProcessGeneST0.0430.0120.055
qa3prime0.0300.0040.035
qaGeneST0.0390.0060.045
regress0.1610.0080.169
regressResult-class0.1420.0140.156
selectSigGene0.1520.0110.165
selectSigGeneInt0.3820.0160.399