Package: clippda

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.4.0.tar.gz

StartedAt: 2012-03-24 00:17:50 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:28:33 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 643.3 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 2.14.2 (2012-02-29)
* 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 '1.4.0'
* 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 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 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 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
** 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
ZvaluescasesVcontrolsPlots	0.020	0.004	0.024
ZvaluesfrommultinomPlots	1.724	0.253	2.018
aclinicalProteomicsData-class	0.116	0.011	0.130
aclinicalProteomicsData-methods	0.356	0.391	0.801
betweensampleVariance	6.038	1.072	7.315
checkNo.replicates	0.419	0.123	0.613
clippda-package	214.206	36.641	257.991
f	0.000	0.001	0.001
fisherInformation	0.155	0.014	0.171
liverRawData	0.032	0.002	0.035
liver_pheno	0.002	0.001	0.003
liverdata	6.948	1.432	8.457
mostSimilarTwo	0.004	0.000	0.005
negativeIntensitiesCorrection	2.256	0.292	2.734
phenoDataFrame	0.120	0.015	0.139
pheno_urine	0.002	0.001	0.003
preProcRepeatedPeakData	5.923	1.315	7.413
proteomicsExprsData	0.558	0.090	0.658
proteomicspData	0.113	0.012	0.125
replicateCorrelations	10.843	1.920	13.202
sampleClusteredData	2.264	0.293	2.700
sampleSize	128.699	22.174	154.089
sampleSize3DscatterPlots	0.034	0.003	0.037
sampleSizeContourPlots	0.063	0.005	0.070
sampleSizeParameters	63.764	10.865	75.500
sample_technicalVariance	15.957	2.508	19.134
spectrumFilter	5.772	1.243	7.310
ztwo	0	0	0