BioC experimental data: CHECK report for HD2013SGI on perceval

Package: HD2013SGI

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HD2013SGI_1.9.1.tar.gz

StartedAt: 2015-08-22 09:24:42 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 09:30:40 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 357.8 seconds

RetCode: 0

Status:  OK

CheckDir: HD2013SGI.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings HD2013SGI_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/HD2013SGI.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HD2013SGI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HD2013SGI’ version ‘1.9.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘RColorBrewer’ ‘gplots’ ‘geneplotter’ ‘splots’ ‘limma’ ‘vcd’ ‘LSD’
  ‘EBImage’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HD2013SGI’ can be installed ... [17s/26s] OK
* checking installed package size ... NOTE
  installed size is 526.8Mb
  sub-directories of 1Mb or more:
    data  524.1Mb
    doc     1.6Mb
* 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
Packages in Depends field not imported from:
  ‘EBImage’ ‘geneplotter’ ‘gplots’ ‘limma’ ‘LSD’ ‘RColorBrewer’
  ‘splots’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘humanReadableNames’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
HD2013SGIHeatmapHuman: no visible global function definition for ‘unit’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘pushViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘viewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.layout’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.rect’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.raster’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘popViewport’
HD2013SGIHeatmapHuman: no visible global function definition for
  ‘grid.text’
HD2013SGIHeatmapHuman: no visible global function definition for ‘gpar’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/77s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
featuresPerWell 40.906  1.723  52.877
datamatrixfull   9.210  0.515  13.119
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/HD2013SGI.Rcheck/00check.log’
for details.

* installing *source* package ‘HD2013SGI’ ...
** 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 (HD2013SGI)

name	user	system	elapsed
HD2013SGI-package	0.087	0.015	0.105
Interactions	0.098	0.006	0.119
QueryAnnotation	0.003	0.000	0.003
TargetAnnotation	0.006	0.002	0.008
datamatrix	0.043	0.011	0.071
datamatrixfull	9.210	0.515	13.119
featuresPerWell	40.906	1.723	52.877
mainEffects	0.443	0.031	0.901
nrOfInteractionsPerTarget	0.006	0.002	0.010
stabilitySelection	0.015	0.042	0.073