Package: methylumi

Version: 1.8.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch methylumi_1.8.0.tar.gz

StartedAt: 2011-10-20 15:25:43 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 15:26:45 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 61.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylumi.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/methylumi.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   methylumi.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/methylumi.Rcheck/00check.log'
for details

* 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	0.97	0.02	0.99
MethyLumiM-class	0	0	0
MethyLumiQC-class	0	0	0
MethyLumiSet-class	0	0	0
extractBarcodeAndPosition	0	0	0
featureFilter	1.45	0.02	1.53
getAssayDataNameSubstitutions	0	0	0
methylumiR	0.85	0.00	0.86
mldat	0.05	0.00	0.05
normalizeMethyLumiSet	0.91	0.01	0.92
plotSampleIntensities	0.08	0.00	0.08
qcplot	0.34	0.00	0.34
varFilter	0.78	0.00	0.78