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BioC 3.5: CHECK report for arrayMvout on oaxaca

This page was generated on 2016-10-26 16:22:03 -0400 (Wed, 26 Oct 2016).

Package 61/1294HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayMvout 1.33.0
V. Carey
Snapshot Date: 2016-10-25 17:15:05 -0400 (Tue, 25 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/arrayMvout
Last Changed Rev: 122712 / Revision: 123034
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: arrayMvout
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings arrayMvout_1.33.0.tar.gz
StartedAt: 2016-10-25 21:40:37 -0700 (Tue, 25 Oct 2016)
EndedAt: 2016-10-25 21:45:37 -0700 (Tue, 25 Oct 2016)
EllapsedTime: 300.0 seconds
RetCode: 0
Status:  OK 
CheckDir: arrayMvout.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings arrayMvout_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/arrayMvout.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘arrayMvout/DESCRIPTION’ ... OK
* this is package ‘arrayMvout’ version ‘1.33.0’
* 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 ‘arrayMvout’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘lumi’ ‘methods’ ‘parody’
  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
.affyArrayOutliers: no visible global function definition for
  ‘sampleNames’
.affyArrayOutliers: no visible global function definition for ‘fitPLM’
.affyArrayOutliers: no visible global function definition for ‘boxplot’
.affyArrayOutliers: no visible global function definition for ‘Mbox’
.affyArrayOutliers: no visible global function definition for
  ‘AffyRNAdeg’
.affyArrayOutliers: no visible global function definition for ‘prcomp’
.affyArrayOutliers : <anonymous>: no visible global function definition
  for ‘mv.calout.detect’
.affyArrayOutliers: no visible global function definition for
  ‘mv.calout.detect’
.lumiArrayOutliers: no visible global function definition for ‘lumiQ’
.lumiArrayOutliers: no visible global function definition for ‘prcomp’
.lumiArrayOutliers: no visible global function definition for
  ‘mv.calout.detect’
.lumiArrayOutliers : <anonymous>: no visible global function definition
  for ‘mv.calout.detect’
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for ‘prcomp’
ArrayOutliers,data.frame-numeric-ANY: no visible global function
  definition for ‘mv.calout.detect’
ArrayOutliers,data.frame-numeric-ANY : <anonymous>: no visible global
  function definition for ‘mv.calout.detect’
plot,arrOutStruct-ANY: no visible global function definition for
  ‘biplot’
plot,arrOutStruct-ANY: no visible global function definition for
  ‘prcomp’
Undefined global functions or variables:
  AffyRNAdeg Mbox biplot boxplot fitPLM lumiQ mv.calout.detect prcomp
  sampleNames
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "biplot", "prcomp")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ArrayOutliers-methods 19.735  0.446  20.568
ArrayOutliers         15.894  0.339  16.240
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/arrayMvout.Rcheck/00check.log’
for details.


arrayMvout.Rcheck/00install.out:

* installing *source* package ‘arrayMvout’ ...
** 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 (arrayMvout)

arrayMvout.Rcheck/arrayMvout-Ex.timings:

nameusersystemelapsed
ArrayOutliers-methods19.735 0.44620.568
ArrayOutliers15.894 0.33916.240
arrOutStruct-class0.1090.0050.114