Package: clippda

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.5.0.tar.gz

StartedAt: 2011-03-17 16:00:11 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:07:24 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 433.3 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/clippda.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.5.0'
* 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 package vignettes in 'inst/doc' ... 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 ...
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
aclinicalProteomicsData-class	0.088	0.005	0.093
aclinicalProteomicsData-methods	0.327	0.255	0.582
betweensampleVariance	4.877	0.071	4.949
checkNo.replicates	0.297	0.021	0.318
clippda-package	166.472	10.112	176.590
fisherInformation	0.106	0.002	0.108
liverRawData	0.021	0.001	0.021
liver_pheno	0.002	0.000	0.002
liverdata	5.142	0.157	5.299
mostSimilarTwo	0.003	0.000	0.003
negativeIntensitiesCorrection	1.685	0.014	1.700
phenoDataFrame	0.081	0.003	0.084
pheno_urine	0.002	0.000	0.002
preProcRepeatedPeakData	4.421	0.090	4.511
proteomicsExprsData	0.414	0.006	0.420
proteomicspData	0.082	0.003	0.085
replicateCorrelations	9.390	0.446	9.836
sampleClusteredData	1.710	0.001	1.712
sampleSize	99.222	5.862	105.087
sampleSize3DscatterPlots	0.070	0.001	0.073
sampleSizeContourPlots	0.048	0.001	0.049
sampleSizeParameters	50.166	3.126	53.293
sample_technicalVariance	12.510	0.733	13.243
spectrumFilter	4.160	0.167	4.327