BioC 2.9: CHECK report for Genominator on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Genominator.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.3Mb
* 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	0.001
addPrimingWeights	5.408	0.100	5.533
aggregateExpData	2.276	0.000	2.303
applyMapped	2.300	0.016	2.382
collapseExpData	3.613	0.064	3.834
computeCoverage	1.292	0.032	1.377
computePrimingWeights	0.244	0.020	0.288
getRegion	0.324	0.008	0.349
importFromAlignedReads	0	0	0
importToExpData	0.672	0.004	0.680
joinExpData	5.944	0.032	6.206
makeGeneRepresentation	0.340	0.000	0.354
mergeWithAnnotation	0.660	0.008	0.699
plot.genominator.coverage	3.944	0.032	4.139
plot.genominator.goodness.of.fit	0.941	0.020	1.092
regionGoodnessOfFit-methods	0.908	0.012	1.274
splitByAnnotation	1.352	0.004	1.699
summarizeByAnnotation	0.676	0.004	0.693
summarizeExpData	0.768	0.004	0.801
validAnnotation	0.016	0.000	0.014
yeastAnno	0.164	0.000	0.162

Summary

Command output