BioC 2.9: CHECK report for RNAinteract on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RNAinteract.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 ‘RNAinteract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RNAinteract’ version ‘1.1.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RNAinteract’ 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 ‘RNAinteract’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: akima
Loading required package: lattice
locfit 1.5-6 	 2010-01-20 

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading Tcl/Tk interface ... done
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘RNAinteract.Rnw’ 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (RNAinteract)

name	user	system	elapsed
RNAinteract-class	0.000	0.000	0.002
bindsamples	0.532	0.008	0.540
computePI	0.04	0.00	0.04
computePValues	0.264	0.008	0.270
embedPCA	0.020	0.000	0.019
estimateMainEffect	1.972	0.020	2.091
getData	0.204	0.004	0.212
getMain	0.008	0.004	0.012
getReplicateData	0.004	0.004	0.011
getSampleNames	0.008	0.000	0.008
getScale	0.012	0.000	0.011
grid.sgiHeatmap	0.116	0.012	0.131
normalizeMainEffectQuery	0.120	0.004	0.128
normalizeMainEffectTemplate	0.556	0.012	0.599
normalizePlateEffect	2.524	0.052	2.576
plotDoublePerturbation	0.100	0.004	0.108
plotHeatmap	0.116	0.000	0.117
reportAnnotation	0.040	0.000	0.037
sgi	0.008	0.000	0.010
sgisubset	0.036	0.000	0.033
startReport	0.04	0.00	0.04
summarizeSamples	0.300	0.000	0.301

Summary

Command output