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BioC experimental data: CHECK report for HD2013SGI on perceval

This page was generated on 2014-04-04 17:29:20 -0700 (Fri, 04 Apr 2014).

Package 85/181HostnameOS / ArchBUILDCHECKBUILD BIN
HD2013SGI 1.2.1
Bernd Fischer
Snapshot Date: 2014-04-04 06:15:32 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_2_13/experiment/pkgs/HD2013SGI
Last Changed Rev: 2684 / Revision: 2768
Last Changed Date: 2014-02-10 09:20:46 -0800 (Mon, 10 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: HD2013SGI
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HD2013SGI_1.2.1.tar.gz
StartedAt: 2014-04-04 11:06:49 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 11:12:02 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 313.2 seconds
RetCode: 0
Status:  OK 
CheckDir: HD2013SGI.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-data-experiment/meat/HD2013SGI.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.2.1’
* 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 ‘HD2013SGI’ can be installed ... [18s/28s] 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 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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [62s/63s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
featuresPerWell 40.720  1.656  42.583
datamatrixfull   9.063  0.370   9.453
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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-package0.2970.0140.315
Interactions0.2620.0070.270
QueryAnnotation0.0100.0020.011
TargetAnnotation0.0130.0030.017
datamatrix0.2610.0090.279
datamatrixfull9.0630.3709.453
featuresPerWell40.720 1.65642.583
mainEffects0.4460.0280.681
nrOfInteractionsPerTarget0.0080.0090.071
stabilitySelection0.0200.0210.184