Package: clippda

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.9.0.tar.gz

StartedAt: 2013-03-25 01:47:57 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:56:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 513.2 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.9.0'
* 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 ... [7s/7s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [428s/429s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          169.685 23.304 193.733
sampleSize               107.295 14.232 121.970
sampleSizeParameters      49.509  6.785  56.438
sample_technicalVariance  10.170  1.373  11.582
replicateCorrelations      9.382  1.115  10.518
spectrumFilter             5.430  1.146   6.604
liverdata                  4.930  1.138   6.096
preProcRepeatedPeakData    4.677  1.006   5.710
betweensampleVariance      4.181  0.842   5.066
* 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	0.022	0.008	0.031
ZvaluesfrommultinomPlots	1.282	0.210	1.512
aclinicalProteomicsData-class	0.076	0.019	0.094
aclinicalProteomicsData-methods	0.269	0.307	0.578
betweensampleVariance	4.181	0.842	5.066
checkNo.replicates	0.253	0.099	0.352
clippda-package	169.685	23.304	193.733
f	0.011	0.012	0.024
fisherInformation	0.119	0.046	0.167
liverRawData	0.011	0.007	0.019
liver_pheno	0.004	0.004	0.008
liverdata	4.930	1.138	6.096
mostSimilarTwo	0.007	0.008	0.015
negativeIntensitiesCorrection	1.861	0.257	2.145
phenoDataFrame	0.091	0.028	0.120
pheno_urine	0.007	0.006	0.013
preProcRepeatedPeakData	4.677	1.006	5.710
proteomicsExprsData	0.338	0.065	0.402
proteomicspData	0.082	0.024	0.108
replicateCorrelations	9.382	1.115	10.518
sampleClusteredData	2.544	0.282	2.827
sampleSize	107.295	14.232	121.970
sampleSize3DscatterPlots	0.056	0.025	0.081
sampleSizeContourPlots	0.071	0.028	0.100
sampleSizeParameters	49.509	6.785	56.438
sample_technicalVariance	10.170	1.373	11.582
spectrumFilter	5.430	1.146	6.604
ztwo	0.006	0.010	0.017