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BioC 3.0: CHECK report for AffyExpress on oaxaca

This page was generated on 2015-04-10 10:02:38 -0700 (Fri, 10 Apr 2015).

Package 19/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyExpress 1.32.0
Xuejun Arthur Li
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/AffyExpress
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: AffyExpress
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyExpress_1.32.0.tar.gz
StartedAt: 2015-04-09 21:11:54 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:13:16 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 82.8 seconds
RetCode: 0
Status:  OK 
CheckDir: AffyExpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AffyExpress_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/AffyExpress.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyExpress/DESCRIPTION’ ... OK
* this is package ‘AffyExpress’ version ‘1.32.0’
* 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 ... [4s/4s] 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 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’ ‘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 png(file = figure1): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure1, height = 960): partial argument
  match of 'file' to 'filename'
AffyQA: warning in matrix(c(1, 3, 5, 7, 2, 4, 6, 7), nr = 4, ncol = 2):
  partial argument match of 'nr' to 'nrow'
AffyQA: warning in png(file = figure2): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure3): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure4): partial argument match of
  'file' to 'filename'
AffyQA: warning in png(file = figure5): partial argument match of
  'file' to 'filename'
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 ‘HTMLInsertGraph’
AffyQA: no visible global function definition for ‘call.exprs’
AffyQA: no visible global function definition for ‘description’
AffyQA: no visible global function definition for ‘description<-’
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 ‘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 ‘exprs’
AffyQA: no visible global function definition for ‘sampleNames<-’
AffyQA: no visible global function definition for ‘fitPLM’
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’
f.test: no visible global function definition for ‘classifyTestsF’
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’
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’
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’
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’
* 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 ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
AffyInteraction 6.471   0.11   6.848
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/AffyExpress.Rcheck/00check.log’
for details.

AffyExpress.Rcheck/00install.out:

* installing *source* package ‘AffyExpress’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AffyExpress)

AffyExpress.Rcheck/AffyExpress-Ex.timings:

nameusersystemelapsed
AffyInteraction6.4710.1106.848
AffyQA0.0010.0000.000
AffyRegress1.7710.0321.855
Filter2.2920.0372.342
import.data0.0010.0010.000
interaction.result2html1.9780.0342.024
make.contrast0.0150.0000.016
make.design0.0080.0010.009
post.interaction1.5790.0141.601
pre.process1.5340.0131.555
regress1.6360.0151.659
result2html1.7460.0321.835
select.sig.gene1.5320.0141.569