Package: ITALICS

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ITALICS_2.18.0.tar.gz

StartedAt: 2013-03-25 00:08:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:11:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 161.0 seconds

RetCode: 0

Status:  OK

CheckDir: ITALICS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ITALICS.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ITALICS/DESCRIPTION' ... OK
* this is package 'ITALICS' version '2.18.0'
* 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 whether package 'ITALICS' 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 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 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 ... NOTE
trainITALICS: warning in list.files(dir, full.name = TRUE): partial
  argument match of 'full.name' to 'full.names'
* checking Rd files ... NOTE
prepare_Rd: GLAD.GLAD.Rd:33: Dropping empty section \keyword
prepare_Rd: ITALICSNew.Rd:82: Dropping empty section \keyword
prepare_Rd: ITALICSTrain.Rd:43: Dropping empty section \keyword
prepare_Rd: Model.GetConfDat.Rd:23: Dropping empty section \keyword
prepare_Rd: Model.GetCorrection.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetEffet.Rd:20: Dropping empty section \keyword
prepare_Rd: Model.GetModel.Rd:21: Dropping empty section \keyword
prepare_Rd: Model.GetResidu.Rd:18: Dropping empty section \keyword
prepare_Rd: New.AddInfo.Rd:24: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:31: Dropping empty section \keyword
prepare_Rd: New.fromQuartetToSnp.Rd:25: Dropping empty section \examples
prepare_Rd: New.fromSnpToQuartet.Rd:25: Dropping empty section \keyword
prepare_Rd: New.getQuartet.Rd:27: Dropping empty section \keyword
prepare_Rd: New.getSnpInfo.Rd:25: Dropping empty section \keyword
prepare_Rd: New.readQuartetCopyNb.Rd:23: Dropping empty section \keyword
* 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'ITALICS-006.pdf' from 272Kb to 41Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'ITALICS-006.pdf'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/ITALICS.Rcheck/00check.log'
for details.

* installing *source* package 'ITALICS' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ITALICS.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (ITALICS)

name	user	system	elapsed
ITALICSNew	0.000	0.001	0.001