BioC 2.9: CHECK report for clippda on pitt

Package: clippda

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.3.0.tar.gz

StartedAt: 2011-07-07 02:22:41 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:34:06 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 685.4 seconds

RetCode: 0

Status: OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/clippda.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under 'inst/doc' ... 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	0.132	0.014	0.148
aclinicalProteomicsData-methods	0.425	0.399	0.841
betweensampleVariance	6.978	1.069	8.183
checkNo.replicates	0.417	0.120	0.549
clippda-package	235.968	35.203	279.374
fisherInformation	0.161	0.013	0.220
liverRawData	0.033	0.002	0.035
liver_pheno	0.003	0.001	0.004
liverdata	7.250	1.422	8.811
mostSimilarTwo	0.004	0.000	0.004
negativeIntensitiesCorrection	2.386	0.272	2.814
phenoDataFrame	0.119	0.010	0.129
pheno_urine	0.002	0.001	0.003
preProcRepeatedPeakData	6.403	1.256	7.996
proteomicsExprsData	0.635	0.092	0.803
proteomicspData	0.120	0.013	0.136
replicateCorrelations	12.839	1.830	14.859
sampleClusteredData	2.412	0.266	2.719
sampleSize	141.284	21.051	166.372
sampleSize3DscatterPlots	0.179	0.005	0.201
sampleSizeContourPlots	0.070	0.004	0.073
sampleSizeParameters	70.228	10.626	83.164
sample_technicalVariance	17.348	2.442	20.162
spectrumFilter	6.136	1.261	7.847

Summary

Command output