Package: CGHbase

Version: 1.15.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHbase_1.15.1.tar.gz

StartedAt: 2012-06-20 22:40:32 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 22:41:49 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 77.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CGHbase.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CGHbase.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CGHbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHbase' version '1.15.1'
* 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 whether package 'CGHbase' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* 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 ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/CGHbase.Rcheck/00_pkg_src/CGHbase/man/CGHbase-package.Rd':
  'WiltingData'

Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/CGHbase.Rcheck/00_pkg_src/CGHbase/man/class.cghCall.Rd':
  'CGHcall'

Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/CGHbase.Rcheck/00_pkg_src/CGHbase/man/class.cghSeg.Rd':
  'segmentData'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'summaryPlot' and siglist 'cghCall,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/CGHbase.Rcheck/00check.log'
for details.

* 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)

name	user	system	elapsed
class.cghCall	0.204	0.004	0.211
class.cghRaw	0.516	0.062	0.598
class.cghRegions	0.550	0.007	0.569
class.cghSeg	0.085	0.002	0.092
copynumber	0.070	0.005	0.078
frequencyPlot	0	0	0
frequencyPlotCalls	0.001	0.000	0.001
make_cghRaw	0.165	0.013	0.186
summaryPlot	0.001	0.000	0.000