BioC 2.7: CHECK report for clippda on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/clippda.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: use of a true value for 'ZipData' is deprecated
See ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/clippda.Rcheck/00install.out’ for details.
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/clippda.Rcheck/00check.log’
for details

* installing *source* package ‘clippda’ ...
** R
** data
Warning: use of a true value for 'ZipData' is deprecated
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
aclinicalProteomicsData-class	0.084	0.004	0.089
aclinicalProteomicsData-methods	0.440	0.224	0.665
betweensampleVariance	5.280	0.064	5.342
checkNo.replicates	0.276	0.020	0.295
clippda-package	169.747	0.188	169.949
fisherInformation	0.168	0.004	0.172
liverRawData	0.012	0.000	0.015
liver_pheno	0.000	0.000	0.002
liverdata	4.336	0.000	4.336
mostSimilarTwo	0.000	0.000	0.002
negativeIntensitiesCorrection	1.376	0.000	1.376
phenoDataFrame	0.076	0.000	0.077
pheno_urine	0.004	0.000	0.002
preProcRepeatedPeakData	3.884	0.004	3.891
proteomicsExprsData	0.548	0.000	0.551
proteomicspData	0.084	0.000	0.081
replicateCorrelations	9.633	0.004	9.634
sampleClusteredData	1.480	0.004	1.485
sampleSize	105.515	0.072	105.598
sampleSize3DscatterPlots	0.132	0.004	0.134
sampleSizeContourPlots	0.036	0.004	0.042
sampleSizeParameters	51.799	0.028	51.829
sample_technicalVariance	13.101	0.016	13.117
spectrumFilter	3.688	0.000	3.688

Summary

Command output