Package: Genominator

Version: 1.7.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch Genominator_1.7.0.tar.gz

StartedAt: 2011-07-07 04:15:34 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 04:18:23 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 168.9 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Genominator.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* 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 '1.7.0'
* 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 ... NOTE
  installed size is 165.5Mb
  sub-directories of 1Mb or more:
    data    1.3Mb
    doc   161.2Mb
* 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 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	0	0
addPrimingWeights	4.96	0.64	6.41
aggregateExpData	1.68	0.00	1.69
applyMapped	2.05	0.00	2.54
collapseExpData	3.09	0.06	3.16
computeCoverage	1.13	0.02	1.15
computePrimingWeights	0.46	0.50	0.96
getRegion	0.33	0.00	0.33
importFromAlignedReads	0	0	0
importToExpData	0.53	0.01	0.56
joinExpData	4.81	0.02	4.83
makeGeneRepresentation	0.35	0.00	0.34
mergeWithAnnotation	0.51	0.00	0.52
plot.genominator.coverage	3.38	0.03	3.42
plot.genominator.goodness.of.fit	0.95	0.00	0.95
regionGoodnessOfFit-methods	0.80	0.02	0.81
splitByAnnotation	1.06	0.00	1.06
summarizeByAnnotation	0.6	0.0	0.6
summarizeExpData	0.62	0.01	0.64
validAnnotation	0.02	0.00	0.01
yeastAnno	0.17	0.02	0.19