Package: methylumi

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methylumi_1.8.0.tar.gz

StartedAt: 2011-10-20 16:02:32 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:03:58 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 86.3 seconds

RetCode: 0

Status:  OK

CheckDir: methylumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/methylumi.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methylumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylumi' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'methylumi' 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 ... NOTE
prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso
prepare_Rd: estimateM.Rd:37-39: 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'methylumi.pdf' from 292Kb to 163Kb
  consider running tools::compactPDF() on these files
* 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 'methylumi' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "summary" in "methylumi"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (methylumi)

name	user	system	elapsed
MethyLumi-class	0.951	0.048	1.187
MethyLumiM-class	0.001	0.000	0.002
MethyLumiQC-class	0.001	0.000	0.002
MethyLumiSet-class	0.001	0.001	0.002
extractBarcodeAndPosition	0.005	0.000	0.005
featureFilter	2.001	0.079	2.167
getAssayDataNameSubstitutions	0.005	0.002	0.006
methylumiR	0.787	0.029	0.855
mldat	0.087	0.003	0.090
normalizeMethyLumiSet	1.190	0.031	1.268
plotSampleIntensities	0.197	0.005	0.203
qcplot	0.478	0.005	0.492
varFilter	1.108	0.008	1.130