Package: Genominator

Version: 1.7.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Genominator_1.7.0.tar.gz

StartedAt: 2011-07-07 00:43:21 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 00:45:37 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 136.3 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Genominator.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.7.0’
* 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 installed package size ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... 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 ...
*** tangling vignette sources ...
   ‘Genominator.Rnw’ 
   ‘plotting.Rnw’ 
   ‘withShortRead.Rnw’ 
** testing if installed package can be loaded

* DONE (Genominator)

name	user	system	elapsed
ExpData	0.000	0.000	0.002
addPrimingWeights	5.376	0.092	5.496
aggregateExpData	2.192	0.000	2.196
applyMapped	2.084	0.020	2.104
collapseExpData	3.585	0.036	3.765
computeCoverage	1.236	0.036	1.275
computePrimingWeights	0.296	0.040	0.335
getRegion	0.376	0.000	0.378
importFromAlignedReads	0	0	0
importToExpData	0.652	0.008	0.661
joinExpData	5.608	0.012	5.625
makeGeneRepresentation	0.316	0.000	0.316
mergeWithAnnotation	0.652	0.000	0.656
plot.genominator.coverage	3.888	0.012	3.901
plot.genominator.goodness.of.fit	0.944	0.020	0.967
regionGoodnessOfFit-methods	0.869	0.020	0.889
splitByAnnotation	1.296	0.004	1.302
summarizeByAnnotation	0.668	0.004	0.672
summarizeExpData	0.812	0.008	0.820
validAnnotation	0.012	0.000	0.015
yeastAnno	0.164	0.000	0.170