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BioC experimental data: CHECK report for HD2013SGI on perceval

This page was generated on 2015-08-22 17:44:51 -0700 (Sat, 22 Aug 2015).

Package 118/246HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HD2013SGI 1.9.1
Bernd Fischer
Snapshot Date: 2015-08-22 06:15:25 -0700 (Sat, 22 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/HD2013SGI
Last Changed Rev: 3322 / Revision: 3391
Last Changed Date: 2015-06-17 08:38:47 -0700 (Wed, 17 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
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 

Summary

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

Command output

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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.


HD2013SGI.Rcheck/00install.out:

* 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)

HD2013SGI.Rcheck/HD2013SGI-Ex.timings:

nameusersystemelapsed
HD2013SGI-package0.0870.0150.105
Interactions0.0980.0060.119
QueryAnnotation0.0030.0000.003
TargetAnnotation0.0060.0020.008
datamatrix0.0430.0110.071
datamatrixfull 9.210 0.51513.119
featuresPerWell40.906 1.72352.877
mainEffects0.4430.0310.901
nrOfInteractionsPerTarget0.0060.0020.010
stabilitySelection0.0150.0420.073