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CHECK report for AffyExpress on merida2

This page was generated on 2018-10-17 08:47:25 -0400 (Wed, 17 Oct 2018).

Package 22/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyExpress 1.46.0
Xuejun Arthur Li
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/AffyExpress
Branch: RELEASE_3_7
Last Commit: 2add4a4
Last Changed Date: 2018-04-30 10:35:07 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AffyExpress
Version: 1.46.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffyExpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffyExpress_1.46.0.tar.gz
StartedAt: 2018-10-16 19:48:07 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:49:10 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 63.8 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AffyExpress.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AffyExpress_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/AffyExpress.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.46.0’
* 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 ‘AffyExpress’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' calls in package code:
  ‘R2HTML’ ‘affyPLM’ ‘annaffy’ ‘gcrma’ ‘genefilter’ ‘simpleaffy’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘affy’ ‘limma’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
  partial argument match of 'nr' to 'nrow'
AffyInteraction: no visible global function definition for ‘pData’
AffyInteraction: no visible global function definition for ‘annotation’
AffyInteraction: no visible global function definition for ‘exprs’
AffyQA: no visible global function definition for ‘pData’
AffyQA: no visible global function definition for ‘cdfName’
AffyQA: no visible global function definition for ‘cleancdfname’
AffyQA: no visible global function definition for ‘setQCEnvironment’
AffyQA: no visible global function definition for ‘qc.get.alpha1’
AffyQA: no visible global function definition for ‘HTMLStart’
AffyQA: no visible global function definition for ‘HTML’
AffyQA: no visible global function definition for ‘as.title’
AffyQA: no visible global function definition for ‘png’
AffyQA: no visible global function definition for ‘plot’
AffyQA: no visible global function definition for ‘text’
AffyQA: no visible global function definition for ‘HTMLInsertGraph’
AffyQA: no visible global function definition for ‘dev.off’
AffyQA: no visible global function definition for ‘call.exprs’
AffyQA: no visible global function definition for ‘layout’
AffyQA: no visible global function definition for ‘par’
AffyQA: no visible global function definition for ‘description’
AffyQA: no visible global function definition for ‘description<-’
AffyQA: no visible global function definition for ‘boxplot’
AffyQA: no visible global function definition for ‘barplot’
AffyQA: no visible global function definition for ‘avbg’
AffyQA: no visible global function definition for ‘percent.present’
AffyQA: no visible global function definition for ‘sfs’
AffyQA: no visible global function definition for ‘spikeInProbes’
AffyQA: no visible global function definition for ‘legend’
AffyQA: no visible global function definition for ‘ratios’
AffyQA: no visible global function definition for ‘AffyRNAdeg’
AffyQA: no visible global function definition for ‘summaryAffyRNAdeg’
AffyQA: no visible global function definition for ‘plotAffyRNAdeg’
AffyQA: no visible global function definition for ‘rma’
AffyQA: no visible global function definition for ‘cor’
AffyQA: no visible global function definition for ‘exprs’
AffyQA: no visible global function definition for ‘hclust’
AffyQA: no visible global function definition for ‘as.dist’
AffyQA: no visible global function definition for ‘sampleNames<-’
AffyQA: no visible global function definition for ‘fitPLM’
AffyQA: no visible global function definition for ‘image’
AffyQA: no visible global function definition for ‘Mbox’
AffyQA: no visible global function definition for ‘package.version’
AffyQA: no visible global function definition for ‘HTMLStop’
AffyRegress: no visible global function definition for ‘annotation’
AffyRegress: no visible global function definition for ‘pData’
Filter: no visible global function definition for ‘exprs’
Filter: no visible global function definition for ‘kOverA’
Filter: no visible global function definition for ‘filterfun’
Filter: no visible global function definition for ‘genefilter’
Filter: no visible binding for global variable ‘IQR’
Filter: no visible global function definition for ‘quantile’
f.test: no visible global function definition for ‘classifyTestsF’
f.test: no visible global function definition for ‘pf’
get.f: no visible global function definition for ‘classifyTestsF’
import.data: no visible global function definition for
  ‘read.AnnotatedDataFrame’
import.data: no visible global function definition for ‘ReadAffy’
import.data: no visible global function definition for ‘pData’
interaction.result2html: no visible global function definition for
  ‘aaf.handler’
interaction.result2html: no visible global function definition for
  ‘aafTableAnn’
interaction.result2html: no visible global function definition for
  ‘aafTable’
interaction.result2html: no visible global function definition for
  ‘saveHTML’
make.design: no visible global function definition for ‘model.matrix’
make.design: no visible global function definition for ‘as.formula’
permute.1: no visible global function definition for ‘lmFit’
permute.1: no visible global function definition for ‘contrasts.fit’
post.interaction: no visible global function definition for ‘pData’
pre.process: no visible global function definition for ‘gcrma’
pre.process: no visible global function definition for ‘rma’
pre.process: no visible global function definition for ‘exprs’
pre.process: no visible global function definition for ‘par’
pre.process: no visible global function definition for ‘hist’
pre.process: no visible global function definition for ‘write.table’
regress: no visible global function definition for ‘lmFit’
regress: no visible global function definition for ‘contrasts.fit’
regress: no visible global function definition for ‘eBayes’
regress: no visible global function definition for ‘p.adjust’
result2html: no visible global function definition for ‘aaf.handler’
result2html: no visible global function definition for ‘aafTableAnn’
result2html: no visible global function definition for ‘aafTable’
result2html: no visible global function definition for ‘saveHTML’
Undefined global functions or variables:
  AffyRNAdeg HTML HTMLInsertGraph HTMLStart HTMLStop IQR Mbox ReadAffy
  aaf.handler aafTable aafTableAnn annotation as.dist as.formula
  as.title avbg barplot boxplot call.exprs cdfName classifyTestsF
  cleancdfname contrasts.fit cor description description<- dev.off
  eBayes exprs filterfun fitPLM gcrma genefilter hclust hist image
  kOverA layout legend lmFit model.matrix p.adjust pData
  package.version par percent.present pf plot plotAffyRNAdeg png
  qc.get.alpha1 quantile ratios read.AnnotatedDataFrame rma
  sampleNames<- saveHTML setQCEnvironment sfs spikeInProbes
  summaryAffyRNAdeg text write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "barplot", "boxplot", "hist", "image", "layout",
             "legend", "par", "plot", "text")
  importFrom("stats", "IQR", "as.dist", "as.formula", "cor", "hclust",
             "model.matrix", "p.adjust", "pf", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/AffyExpress.Rcheck/00check.log’
for details.



Installation output

AffyExpress.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AffyExpress
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AffyExpress’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AffyExpress)

Tests output


Example timings

AffyExpress.Rcheck/AffyExpress-Ex.timings

nameusersystemelapsed
AffyInteraction4.3680.1654.588
AffyQA0.0020.0000.002
AffyRegress1.6180.0201.643
Filter3.1230.0703.214
import.data0.0020.0000.002
interaction.result2html1.6790.0231.714
make.contrast0.3110.0010.313
make.design0.010.000.01
post.interaction1.4280.0131.450
pre.process1.4530.0141.482
regress1.3910.0151.420
result2html1.5190.0251.557
select.sig.gene1.4340.0221.462