Package: Genominator

Version: 1.4.2

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings Genominator_1.4.2.tar.gz

StartedAt: 2011-03-31 08:09:39 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 08:12:12 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 153.3 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/Genominator.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 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.4.2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Genominator' can be installed ... 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 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

* installing *source* package 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: DBI

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

Loading required package: biomaRt
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0	0	0
addPrimingWeights	3.75	0.59	4.52
aggregateExpData	1.32	0.02	1.33
applyMapped	1.37	0.00	1.44
collapseExpData	2.61	0.04	2.65
computeCoverage	0.91	0.00	0.91
computePrimingWeights	0.44	0.27	0.70
getRegion	0.21	0.00	0.22
importFromAlignedReads	0	0	0
importToExpData	0.55	0.00	0.55
joinExpData	3.67	0.01	3.69
makeGeneRepresentation	0.26	0.00	0.27
mergeWithAnnotation	0.44	0.02	0.45
plot.genominator.coverage	2.91	0.05	2.95
plot.genominator.goodness.of.fit	0.72	0.04	0.77
regionGoodnessOfFit-methods	0.65	0.01	0.67
splitByAnnotation	0.77	0.00	0.76
summarizeByAnnotation	0.39	0.00	0.44
summarizeExpData	0.50	0.02	0.52
validAnnotation	0.01	0.00	0.01
yeastAnno	0.18	0.02	0.19