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: 2013-03-25 00:49:12 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:58:48 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 576.0 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ... [8s/8s] 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 ... [476s/487s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          210.342  0.400 216.845
sampleSize               128.104  0.196 129.574
sampleSizeParameters      62.536  0.156  64.923
sample_technicalVariance  12.585  0.052  12.741
replicateCorrelations     11.401  0.004  11.421
liverdata                  9.848  0.008  10.003
preProcRepeatedPeakData    9.005  0.008   9.014
betweensampleVariance      8.184  0.124   8.406
spectrumFilter             7.940  0.016   8.080
* 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	0.024	0.004	0.027
ZvaluesfrommultinomPlots	2.344	0.024	2.405
aclinicalProteomicsData-class	0.26	0.00	0.26
aclinicalProteomicsData-methods	0.604	0.188	0.790
betweensampleVariance	8.184	0.124	8.406
checkNo.replicates	0.712	0.012	0.723
clippda-package	210.342	0.400	216.845
f	0.024	0.000	0.024
fisherInformation	0.172	0.004	0.179
liverRawData	0.02	0.00	0.02
liver_pheno	0.012	0.004	0.016
liverdata	9.848	0.008	10.003
mostSimilarTwo	0.02	0.00	0.02
negativeIntensitiesCorrection	3.084	0.000	3.084
phenoDataFrame	0.176	0.000	0.174
pheno_urine	0.032	0.000	0.030
preProcRepeatedPeakData	9.005	0.008	9.014
proteomicsExprsData	0.436	0.000	0.436
proteomicspData	0.132	0.004	0.137
replicateCorrelations	11.401	0.004	11.421
sampleClusteredData	3.164	0.000	3.166
sampleSize	128.104	0.196	129.574
sampleSize3DscatterPlots	0.088	0.000	0.089
sampleSizeContourPlots	0.124	0.004	0.128
sampleSizeParameters	62.536	0.156	64.923
sample_technicalVariance	12.585	0.052	12.741
spectrumFilter	7.940	0.016	8.080
ztwo	0.016	0.000	0.013