Package: AffyExpress

Version: 1.48.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AffyExpress.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AffyExpress_1.48.0.tar.gz

StartedAt: 2019-04-15 22:07:19 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:08:29 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 69.2 seconds

RetCode: 0

Status:  OK

CheckDir: AffyExpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:AffyExpress.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings AffyExpress_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/AffyExpress.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.48.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
AffyInteraction 7.588  0.124   8.868
Filter          5.476  0.028   5.517
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/AffyExpress.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL AffyExpress
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

name	user	system	elapsed
AffyInteraction	7.588	0.124	8.868
AffyQA	0.000	0.000	0.001
AffyRegress	3.644	0.004	3.673
Filter	5.476	0.028	5.517
import.data	0	0	0
interaction.result2html	3.940	0.008	3.962
make.contrast	0.396	0.000	0.394
make.design	0.008	0.000	0.007
post.interaction	3.784	0.008	3.831
pre.process	3.448	0.004	3.476
regress	3.160	0.004	3.181
result2html	3.124	0.008	3.145
select.sig.gene	3.188	0.012	3.209