Package: Genominator

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.5.1.tar.gz

StartedAt: 2011-02-24 15:48:25 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:50:04 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 98.8 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/Genominator.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 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 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	0.076	0.000	0.076
addPrimingWeights	3.207	0.054	3.272
aggregateExpData	1.167	0.012	1.232
applyMapped	1.429	0.009	1.439
collapseExpData	2.621	0.076	2.742
computeCoverage	0.910	0.026	0.935
computePrimingWeights	0.354	0.027	0.379
getRegion	0.171	0.003	0.174
importFromAlignedReads	0.000	0.000	0.001
importToExpData	0.382	0.004	0.387
joinExpData	3.075	0.035	4.332
makeGeneRepresentation	0.329	0.001	0.330
mergeWithAnnotation	0.340	0.002	0.437
plot.genominator.coverage	2.683	0.048	2.823
plot.genominator.goodness.of.fit	0.716	0.032	0.768
regionGoodnessOfFit-methods	0.649	0.020	0.669
splitByAnnotation	0.642	0.005	0.649
summarizeByAnnotation	0.349	0.004	0.442
summarizeExpData	0.495	0.008	0.502
validAnnotation	0.019	0.001	0.020
yeastAnno	0.249	0.007	0.256