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BioC 3.1: CHECK report for ArrayTools on zin2

This page was generated on 2015-10-09 09:23:40 -0700 (Fri, 09 Oct 2015).

Package 56/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayTools 1.28.0
Arthur Li
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ArrayTools
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayTools
Version: 1.28.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.28.0.tar.gz
StartedAt: 2015-10-08 22:33:18 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:34:05 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 47.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ArrayTools_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ArrayTools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ‘1.28.0’
* 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 ... [3s/3s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘R2HTML’ ‘affyPLM’ ‘annaffy’ ‘gcrma’ ‘simpleaffy’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
createIndex: no visible global function definition for ‘HTMLStart’
createIndex: no visible global function definition for ‘as.title’
createIndex: no visible global function definition for ‘HTML’
createIndex: no visible global function definition for ‘HTMLStop’
geneFilter: no visible global function definition for ‘getText’
geneFilter: no visible global function definition for ‘aafSymbol’
geneFilter: no visible global function definition for ‘aafDescription’
geneFilter: no visible global function definition for ‘aafChromosome’
geneFilter: no visible global function definition for ‘aafGenBank’
geneFilter: no visible global function definition for ‘aafCytoband’
geneFilter: no visible global function definition for ‘aafUniGene’
geneFilter: no visible global function definition for ‘aafPubMed’
geneFilter: no visible global function definition for ‘aafLocusLink’
output.ing: no visible global function definition for ‘getText’
output.ing: no visible global function definition for ‘aafSymbol’
output.ing: no visible global function definition for ‘aafDescription’
output.ing: no visible global function definition for ‘aafChromosome’
output.ing: no visible global function definition for ‘aafGenBank’
output.ing: no visible global function definition for ‘aafCytoband’
output.ing: no visible global function definition for ‘aafUniGene’
output.ing: no visible global function definition for ‘aafPubMed’
output.ing: no visible global function definition for ‘aafLocusLink’
preProcess3prime: no visible global function definition for ‘gcrma’
preProcess3prime: no visible global function definition for ‘getText’
preProcess3prime: no visible global function definition for ‘aafSymbol’
preProcess3prime: no visible global function definition for
  ‘aafDescription’
preProcess3prime: no visible global function definition for
  ‘aafChromosome’
preProcess3prime: no visible global function definition for
  ‘aafGenBank’
preProcess3prime: no visible global function definition for
  ‘aafCytoband’
preProcess3prime: no visible global function definition for
  ‘aafUniGene’
preProcess3prime: no visible global function definition for ‘aafPubMed’
preProcess3prime: no visible global function definition for
  ‘aafLocusLink’
preProcessGeneST: no visible binding for global variable
  ‘hugene10stCONTROL’
preProcessGeneST: no visible binding for global variable
  ‘mogene10stCONTROL’
preProcessGeneST: no visible global function definition for ‘getText’
preProcessGeneST: no visible global function definition for ‘aafSymbol’
preProcessGeneST: no visible global function definition for
  ‘aafDescription’
preProcessGeneST: no visible global function definition for
  ‘aafChromosome’
preProcessGeneST: no visible global function definition for
  ‘aafGenBank’
preProcessGeneST: no visible global function definition for
  ‘aafCytoband’
preProcessGeneST: no visible global function definition for
  ‘aafUniGene’
preProcessGeneST: no visible global function definition for ‘aafPubMed’
preProcessGeneST: no visible global function definition for
  ‘aafLocusLink’
qa3prime: no visible global function definition for ‘setQCEnvironment’
qa3prime: no visible global function definition for ‘qc.get.alpha1’
qa3prime: no visible global function definition for ‘HTMLStart’
qa3prime: no visible global function definition for ‘as.title’
qa3prime: no visible global function definition for ‘HTML’
qa3prime: no visible global function definition for ‘HTMLInsertGraph’
qa3prime: no visible global function definition for ‘call.exprs’
qa3prime: no visible global function definition for ‘avbg’
qa3prime: no visible global function definition for ‘percent.present’
qa3prime: no visible global function definition for ‘sfs’
qa3prime: no visible global function definition for ‘spikeInProbes’
qa3prime: no visible global function definition for ‘ratios’
qa3prime: no visible global function definition for ‘fitPLM’
qa3prime: no visible global function definition for ‘HTMLStop’
qaGeneST: no visible global function definition for ‘HTMLStart’
qaGeneST: no visible global function definition for ‘as.title’
qaGeneST: no visible global function definition for ‘HTML’
qaGeneST: no visible global function definition for ‘HTMLInsertGraph’
qaGeneST: no visible global function definition for ‘HTMLStop’
regress: no visible global function definition for ‘permute.1’
regress: no visible binding for global variable ‘design’
Output2HTML,interactionResult : .local: no visible global function
  definition for ‘aaf.handler’
Output2HTML,interactionResult : .local: no visible global function
  definition for ‘aafTableAnn’
Output2HTML,interactionResult : .local: no visible global function
  definition for ‘aafTable’
Output2HTML,interactionResult : .local: no visible global function
  definition for ‘saveHTML’
Output2HTML,regressResult : .local: no visible global function
  definition for ‘aaf.handler’
Output2HTML,regressResult : .local: no visible global function
  definition for ‘aafTableAnn’
Output2HTML,regressResult : .local: no visible global function
  definition for ‘aafTable’
Output2HTML,regressResult : .local: no visible global function
  definition for ‘saveHTML’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-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
Output2HTML0.0930.0000.093
QC0.0020.0000.001
Sort0.060.000.06
contrastMatrix-class0.0280.0040.032
createExpressionSet0.0640.0000.064
createGSEAFiles0.0040.0000.004
createIndex0.2180.0000.218
createIngenuityFile0.0530.0000.054
designMatrix-class0.0130.0000.012
eSetExample0.0030.0000.004
exprsExample0.0030.0000.002
geneFilter2.4560.0322.494
interactionResult-class0.1530.0030.158
pDataExample0.0020.0000.002
postInteraction0.1570.0000.156
preProcess3prime3.5600.0923.674
preProcessGeneST0.0090.0000.009
qa3prime0.0010.0000.001
qaGeneST0.0080.0000.008
regress0.0470.0000.047
regressResult-class0.0490.0000.049
selectSigGene0.0560.0000.056
selectSigGeneInt0.1700.0040.174