Package: SNPchip

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SNPchip_1.15.0.tar.gz

StartedAt: 2011-03-17 17:35:49 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:37:35 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 105.7 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/SNPchip.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SNPchip/DESCRIPTION' ... OK
* this is package 'SNPchip' version '1.15.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SNPchip' 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
prepare_Rd: sample.snpset.Rd:10-11: Dropping empty section \details
prepare_Rd: sample.snpset.Rd:12-13: Dropping empty section \source
prepare_Rd: sample.snpset.Rd:14-15: Dropping empty section \references
prepare_Rd: showSummary.Rd:21-22: Dropping empty section \details
prepare_Rd: showSummary.Rd:23-24: Dropping empty section \value
prepare_Rd: showSummary.Rd:27-28: Dropping empty section \note
prepare_Rd: showSummary.Rd:25: Dropping empty section \references
prepare_Rd: showSummary.Rd:31-32: Dropping empty section \examples
* 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 ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.13.18
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'SNPchip' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

================================================================================
Welcome to oligoClasses version 1.13.18
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Creating a new generic function for "summary" in "SNPchip"
Creating a new generic function for "plot" in "SNPchip"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.13.18
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to SNPchip version 1.15.0

* DONE (SNPchip)

name	user	system	elapsed
ParESet-class	0.001	0.000	0.001
ParSnpCallSet-class	0.000	0.001	0.001
ParSnpCopyNumberSet-class	0.099	0.000	0.099
ParSnpSet-class	0.000	0.001	0.001
centromere	0.005	0.001	0.005
chromosomeAnnotation	0.018	0.001	0.020
chromosomeSize	0.004	0.000	0.004
crlmmOut	0.055	0.001	0.056
cytoband	0.004	0.000	0.004
dbSnpId	0	0	0
hapmap	0.040	0.002	0.041
integer2chromosome	0	0	0
plotCytoband	0.052	0.005	0.057
plotPredictions	0	0	0
plotSnp	0.371	0.004	0.375
sample.snpset	0.088	0.002	0.090
snpPar	0.172	0.003	0.175