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BioC 3.4: CHECK report for ArrayTools on moscato1

This page was generated on 2016-09-21 03:42:36 -0700 (Wed, 21 Sep 2016).

Package 62/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayTools 1.33.1
Arthur Li
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayTools
Last Changed Rev: 120597 / Revision: 121152
Last Changed Date: 2016-08-30 15:01:57 -0700 (Tue, 30 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: ArrayTools
Version: 1.33.1
Command: rm -rf ArrayTools.buildbin-libdir ArrayTools.Rcheck && mkdir ArrayTools.buildbin-libdir ArrayTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayTools.buildbin-libdir ArrayTools_1.33.1.tar.gz >ArrayTools.Rcheck\00install.out 2>&1 && cp ArrayTools.Rcheck\00install.out ArrayTools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ArrayTools.buildbin-libdir --install="check:ArrayTools-install.out" --force-multiarch --no-vignettes --timings ArrayTools_1.33.1.tar.gz
StartedAt: 2016-09-20 04:03:11 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:04:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 103.5 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ArrayTools.buildbin-libdir ArrayTools.Rcheck && mkdir ArrayTools.buildbin-libdir ArrayTools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayTools.buildbin-libdir ArrayTools_1.33.1.tar.gz >ArrayTools.Rcheck\00install.out 2>&1 && cp ArrayTools.Rcheck\00install.out ArrayTools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=ArrayTools.buildbin-libdir --install="check:ArrayTools-install.out" --force-multiarch --no-vignettes --timings ArrayTools_1.33.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/ArrayTools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' version '1.33.1'
* 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 whether package 'ArrayTools' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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: no visible global function definition
  for 'aaf.handler'
Output2HTML,interactionResult: no visible global function definition
  for 'aafTableAnn'
Output2HTML,interactionResult: no visible global function definition
  for 'aafTable'
Output2HTML,interactionResult: no visible global function definition
  for 'saveHTML'
Output2HTML,regressResult: no visible global function definition for
  'aaf.handler'
Output2HTML,regressResult: no visible global function definition for
  'aafTableAnn'
Output2HTML,regressResult: no visible global function definition for
  'aafTable'
Output2HTML,regressResult: no visible global function definition for
  'saveHTML'
Undefined global functions or variables:
  HTML HTMLInsertGraph HTMLStart HTMLStop aaf.handler aafChromosome
  aafCytoband aafDescription aafGenBank aafLocusLink aafPubMed
  aafSymbol aafTable aafTableAnn aafUniGene as.title avbg call.exprs
  design fitPLM gcrma getText hugene10stCONTROL mogene10stCONTROL
  percent.present permute.1 qc.get.alpha1 ratios saveHTML
  setQCEnvironment sfs spikeInProbes
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/ArrayTools.Rcheck/00check.log'
for details.


ArrayTools.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ArrayTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayTools' as ArrayTools_1.33.1.zip
* DONE (ArrayTools)

ArrayTools.Rcheck/examples_i386/ArrayTools-Ex.timings:

nameusersystemelapsed
Output2HTML0.060.020.08
QC000
Sort0.050.000.05
contrastMatrix-class0.030.000.03
createExpressionSet0.050.010.06
createGSEAFiles000
createIndex0.170.000.17
createIngenuityFile0.050.000.05
designMatrix-class0.020.000.01
eSetExample0.010.000.02
exprsExample000
geneFilter3.170.053.21
interactionResult-class0.160.000.16
pDataExample000
postInteraction0.140.010.15
preProcess3prime3.690.053.75
preProcessGeneST0.030.000.03
qa3prime000
qaGeneST0.000.030.03
regress0.050.000.05
regressResult-class0.050.000.04
selectSigGene0.050.000.04
selectSigGeneInt0.140.030.18

ArrayTools.Rcheck/examples_x64/ArrayTools-Ex.timings:

nameusersystemelapsed
Output2HTML0.110.000.11
QC000
Sort0.040.010.07
contrastMatrix-class0.050.000.04
createExpressionSet0.060.000.06
createGSEAFiles000
createIndex0.220.020.24
createIngenuityFile0.060.000.06
designMatrix-class0.020.000.02
eSetExample000
exprsExample000
geneFilter3.430.053.50
interactionResult-class0.390.000.39
pDataExample0.010.000.01
postInteraction0.170.000.19
preProcess3prime3.840.033.88
preProcessGeneST0.360.030.39
qa3prime000
qaGeneST0.030.000.04
regress0.080.000.07
regressResult-class0.080.000.08
selectSigGene0.080.000.08
selectSigGeneInt0.210.000.22