Package: clippda

Version: 1.9.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.9.0.tar.gz

StartedAt: 2013-01-16 01:36:03 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:43:14 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 430.7 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clippda’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          163.646  0.228 163.890
sampleSize               100.198  0.160 100.381
sampleSizeParameters      48.387  0.132  48.527
sample_technicalVariance  10.653  0.024  10.673
replicateCorrelations      8.661  0.004   8.662
liverdata                  7.165  0.004   7.170
betweensampleVariance      6.836  0.008   6.845
spectrumFilter             6.257  0.004   6.261
preProcRepeatedPeakData    6.180  0.004   6.186
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘clippda.Rnw’ 
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.020	0.000	0.021
ZvaluesfrommultinomPlots	1.692	0.020	1.712
aclinicalProteomicsData-class	0.096	0.000	0.097
aclinicalProteomicsData-methods	0.388	0.160	0.552
betweensampleVariance	6.836	0.008	6.845
checkNo.replicates	0.592	0.008	0.599
clippda-package	163.646	0.228	163.890
f	0.016	0.000	0.015
fisherInformation	0.140	0.000	0.138
liverRawData	0.012	0.000	0.015
liver_pheno	0.012	0.000	0.011
liverdata	7.165	0.004	7.170
mostSimilarTwo	0.012	0.000	0.012
negativeIntensitiesCorrection	2.192	0.000	2.192
phenoDataFrame	0.108	0.000	0.106
pheno_urine	0.012	0.000	0.012
preProcRepeatedPeakData	6.180	0.004	6.186
proteomicsExprsData	0.288	0.004	0.293
proteomicspData	0.088	0.004	0.097
replicateCorrelations	8.661	0.004	8.662
sampleClusteredData	2.144	0.000	2.151
sampleSize	100.198	0.160	100.381
sampleSize3DscatterPlots	0.044	0.004	0.046
sampleSizeContourPlots	0.076	0.000	0.074
sampleSizeParameters	48.387	0.132	48.527
sample_technicalVariance	10.653	0.024	10.673
spectrumFilter	6.257	0.004	6.261
ztwo	0.008	0.000	0.007