Package: MassArray

Version: 1.2.0

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings MassArray_1.2.0.tar.gz

StartedAt: 2011-03-31 09:10:40 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 09:12:33 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 112.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MassArray.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/MassArray.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MassArray/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MassArray' version '1.2.0'
* checking package name space information ...Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
 OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'MassArray' can be installed ... WARNING
Found the following significant warnings:
  Warning: unknown namespace directive: S3Method(plot, MassArrayData)
  Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
  Warning: unknown namespace directive: S3Method(plot, MassArrayData)
  Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
See 'D:/biocbld/bbs-2.7-bioc/meat/MassArray.Rcheck/00install.out' for details.
* 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 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 ... OK
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.7-bioc/meat/MassArray.Rcheck/00check.log'
for details

* installing *source* package 'MassArray' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
** help
*** installing help indices
** building package indices ...
Warning: unknown namespace directive: S3Method(plot, MassArrayData)
Warning: unknown namespace directive: S3Method(sum, MassArraySpectrum)
** testing if installed package can be loaded

* DONE (MassArray)

name	user	system	elapsed
MassArray.example.data	0.02	0.00	0.01
MassArrayData-class	0	0	0
MassArrayFragment-class	0	0	0
MassArrayPeak-class	0	0	0
MassArraySpectrum-class	0	0	0
ampliconPrediction	2.12	0.01	2.14
analyzeCpGs	0.2	0.0	0.2
bisConvert	0	0	0
calcMW	0	0	0
calcMeth	0	0	0
calcPercentAdduct	0.06	0.00	0.06
calcPercentConversion	0.05	0.00	0.05
combine	4.86	0.00	4.86
convControl	0.03	0.00	0.03
countCGs	0	0	0
createWiggle	0.01	0.00	0.01
estimatePrimerDimer	0.1	0.0	0.1
evaluateSNPs	26.98	0.02	27.00
expandSequence	0	0	0
findCollisions	0	0	0
findFragments	0.02	0.00	0.01
findPeaks	0	0	0
identifySNPs	0.03	0.00	0.03
inSilicoFragmentation	0	0	0
isAssayable	0	0	0
numCollisions	0	0	0
plot.MassArrayData	0.03	0.01	0.05
position	0.03	0.00	0.03
revComplement	0	0	0
rnaDigest	0	0	0
samples	0.03	0.00	0.03
sum.MassArraySpectrum	0.74	0.00	1.66