Package: Genominator

Version: 1.5.1

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings Genominator_1.5.1.tar.gz

StartedAt: 2011-02-24 18:12:15 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:14:20 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 125.0 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/Genominator.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.5.1'
* 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, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

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	3.64	0.64	4.41
aggregateExpData	1.41	0.02	1.75
applyMapped	1.59	0.01	1.62
collapseExpData	2.84	0.03	3.08
computeCoverage	0.95	0.02	1.01
computePrimingWeights	0.67	0.25	0.99
getRegion	0.23	0.00	0.43
importFromAlignedReads	0	0	0
importToExpData	0.44	0.03	0.49
joinExpData	3.66	0.03	3.86
makeGeneRepresentation	0.28	0.00	0.29
mergeWithAnnotation	0.42	0.01	0.44
plot.genominator.coverage	3.02	0.02	3.08
plot.genominator.goodness.of.fit	0.86	0.03	0.94
regionGoodnessOfFit-methods	0.81	0.00	0.81
splitByAnnotation	0.81	0.00	0.81
summarizeByAnnotation	0.44	0.00	0.44
summarizeExpData	0.54	0.02	0.56
validAnnotation	0.02	0.00	0.01
yeastAnno	0.28	0.00	0.29