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BioC 2.13: CHECK report for CGHbase on perceval

This page was generated on 2014-04-05 09:52:07 -0700 (Sat, 05 Apr 2014).

Package 120/750HostnameOS / ArchBUILDCHECKBUILD BIN
CGHbase 1.22.0
Mark van de Wiel
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/CGHbase
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
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: CGHbase
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHbase_1.22.0.tar.gz
StartedAt: 2014-04-05 00:07:48 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:09:00 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 72.5 seconds
RetCode: 0
Status:  OK 
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/CGHbase.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 ‘CGHbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHbase’ version ‘1.22.0’
* 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 ‘CGHbase’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package 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
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
‘:::’ call which should be ‘::’: ‘Biobase:::assayDataElement’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘Biobase:::assayDataDims’
  See the note in ?`:::` about the use of this operator.
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 examples ... [4s/5s] OK
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/CGHbase.Rcheck/00check.log’
for details.

CGHbase.Rcheck/00install.out:

* installing *source* package ‘CGHbase’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CGHbase)

CGHbase.Rcheck/CGHbase-Ex.timings:

nameusersystemelapsed
class.cghCall0.1340.0060.140
class.cghRaw0.6990.0430.743
class.cghRegions0.4210.0080.431
class.cghSeg0.0850.0010.086
copynumber0.0560.0130.069
frequencyPlot0.0070.0010.008
frequencyPlotCalls0.0130.0010.013
make_cghRaw0.2050.0050.223
summaryPlot0.0160.0000.016