Package: SNPchip

Version: 1.16.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings SNPchip_1.16.0.tar.gz

StartedAt: 2011-10-20 14:36:16 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:38:25 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 129.0 seconds

RetCode: 0

Status:  OK

CheckDir: SNPchip.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/SNPchip.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SNPchip/DESCRIPTION’ ... OK
* this is package ‘SNPchip’ version ‘1.16.0’
* checking package namespace 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 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
plotCytoband: no visible binding for global variable ‘lsegments’
plotCytoband: no visible binding for global variable ‘lpolygon’
* 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 1.14.0
  ================================================================================
  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 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

* installing *source* package ‘SNPchip’ ...
** R
** data
** inst
** preparing package for lazy loading
================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
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 1.14.0
================================================================================
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 1.16.0

* DONE (SNPchip)

name	user	system	elapsed
ParESet-class	0.004	0.000	0.002
ParSnpCallSet-class	0.000	0.000	0.001
ParSnpCopyNumberSet-class	0.004	0.000	0.001
ParSnpSet-class	0.000	0.000	0.001
centromere	0.008	0.000	0.005
chromosomeAnnotation	0.016	0.004	0.023
chromosomeSize	0.004	0.000	0.005
crlmmOut	0.040	0.000	0.038
cytoband	0.004	0.000	0.003
dbSnpId	0.000	0.000	0.001
hapmap	0.024	0.004	0.028
integer2chromosome	0	0	0
plotCytoband	0.048	0.004	0.054
plotPredictions	0	0	0
plotSnp	0.652	0.008	0.724
sample.snpset	0.060	0.004	0.062
snpPar	0.356	0.000	0.354