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BioC 3.4: CHECK report for arrayMvout on moscato1

This page was generated on 2016-09-21 03:42:39 -0700 (Wed, 21 Sep 2016).

Package 59/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
arrayMvout 1.31.0
V. Carey
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/arrayMvout
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 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: arrayMvout
Version: 1.31.0
Command: rm -rf arrayMvout.buildbin-libdir arrayMvout.Rcheck && mkdir arrayMvout.buildbin-libdir arrayMvout.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayMvout.buildbin-libdir arrayMvout_1.31.0.tar.gz >arrayMvout.Rcheck\00install.out 2>&1 && cp arrayMvout.Rcheck\00install.out arrayMvout-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=arrayMvout.buildbin-libdir --install="check:arrayMvout-install.out" --force-multiarch --no-vignettes --timings arrayMvout_1.31.0.tar.gz
StartedAt: 2016-09-20 04:00:45 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:07:57 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 432.6 seconds
RetCode: 0
Status:  OK  
CheckDir: arrayMvout.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf arrayMvout.buildbin-libdir arrayMvout.Rcheck && mkdir arrayMvout.buildbin-libdir arrayMvout.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=arrayMvout.buildbin-libdir arrayMvout_1.31.0.tar.gz >arrayMvout.Rcheck\00install.out 2>&1 && cp arrayMvout.Rcheck\00install.out arrayMvout-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=arrayMvout.buildbin-libdir --install="check:arrayMvout-install.out" --force-multiarch --no-vignettes --timings arrayMvout_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/arrayMvout.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 'arrayMvout/DESCRIPTION' ... OK
* this is package 'arrayMvout' version '1.31.0'
* 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 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
* 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ArrayOutliers-methods 23.90   0.27   34.65
ArrayOutliers         21.39   0.17   21.56
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ArrayOutliers-methods 24.13   0.33   24.49
ArrayOutliers         20.89   0.17   21.06
* 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/arrayMvout.Rcheck/00check.log'
for details.


arrayMvout.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'arrayMvout' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'arrayMvout' as arrayMvout_1.31.0.zip
* DONE (arrayMvout)

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

nameusersystemelapsed
ArrayOutliers-methods23.90 0.2734.65
ArrayOutliers21.39 0.1721.56
arrOutStruct-class0.080.000.08

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

nameusersystemelapsed
ArrayOutliers-methods24.13 0.3324.49
ArrayOutliers20.89 0.1721.06
arrOutStruct-class0.110.000.11