BioC 2.9: CHECK report for clippda on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/clippda.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 ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.3.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘clippda’ 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 ... NOTE
Found the following CITATION file(s) in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘clippda.Rnw’ 
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
aclinicalProteomicsData-class	0.172	0.004	0.177
aclinicalProteomicsData-methods	0.492	0.184	0.676
betweensampleVariance	6.284	0.036	6.324
checkNo.replicates	0.316	0.004	0.321
clippda-package	166.138	0.272	167.250
fisherInformation	0.116	0.004	0.117
liverRawData	0.012	0.004	0.015
liver_pheno	0.000	0.000	0.002
liverdata	4.637	0.008	4.707
mostSimilarTwo	0.000	0.000	0.003
negativeIntensitiesCorrection	1.460	0.000	1.488
phenoDataFrame	0.080	0.004	0.084
pheno_urine	0.004	0.000	0.002
preProcRepeatedPeakData	4.076	0.000	4.077
proteomicsExprsData	0.496	0.000	0.494
proteomicspData	0.084	0.004	0.087
replicateCorrelations	9.925	0.000	9.928
sampleClusteredData	1.62	0.00	1.62
sampleSize	105.822	0.140	107.185
sampleSize3DscatterPlots	0.052	0.000	0.054
sampleSizeContourPlots	0.044	0.000	0.044
sampleSizeParameters	49.992	0.048	50.340
sample_technicalVariance	13.104	0.024	13.175
spectrumFilter	3.981	0.000	4.042

Summary

Command output