Package: Genominator

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings Genominator_1.2.0.tar.gz

StartedAt: 2010-10-04 17:13:48 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:16:08 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 139.4 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/Genominator.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.2.0'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking tests ...
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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, 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	0.002	0.000	0.002
addPrimingWeights	4.165	0.114	4.335
aggregateExpData	1.386	0.030	1.578
applyMapped	1.797	0.110	2.071
collapseExpData	3.250	0.171	3.665
computeCoverage	1.179	0.059	1.256
computePrimingWeights	0.538	0.046	0.593
getRegion	0.220	0.005	0.225
importFromAlignedReads	0	0	0
importToExpData	0.485	0.015	0.515
joinExpData	3.790	0.078	4.258
makeGeneRepresentation	0.539	0.008	0.554
mergeWithAnnotation	0.463	0.008	0.475
plot.genominator.coverage	3.682	0.165	3.902
plot.genominator.goodness.of.fit	0.965	0.070	1.043
regionGoodnessOfFit-methods	0.894	0.067	0.969
splitByAnnotation	0.786	0.012	0.893
summarizeByAnnotation	0.425	0.008	0.438
summarizeExpData	0.608	0.013	0.625
validAnnotation	0.025	0.002	0.028
yeastAnno	0.331	0.015	0.353