Package: clippda

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.2.0.tar.gz

StartedAt: 2011-10-20 14:16:53 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:28:40 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 707.3 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 2.13.2 (2011-09-30)
* 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 '1.2.0'
* checking package namespace 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 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 ...
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
aclinicalProteomicsData-class	0.122	0.012	0.195
aclinicalProteomicsData-methods	0.406	0.390	0.963
betweensampleVariance	6.962	1.040	11.350
checkNo.replicates	0.408	0.111	0.854
clippda-package	230.255	35.791	291.584
fisherInformation	0.206	0.018	0.259
liverRawData	0.032	0.003	0.070
liver_pheno	0.002	0.001	0.003
liverdata	7.052	1.360	8.560
mostSimilarTwo	0.003	0.000	0.004
negativeIntensitiesCorrection	2.337	0.265	2.612
phenoDataFrame	0.118	0.012	0.130
pheno_urine	0.003	0.001	0.004
preProcRepeatedPeakData	6.238	1.224	7.600
proteomicsExprsData	0.665	0.087	0.774
proteomicspData	0.118	0.014	0.138
replicateCorrelations	12.613	1.820	14.799
sampleClusteredData	2.409	0.264	2.868
sampleSize	139.637	21.240	164.051
sampleSize3DscatterPlots	0.106	0.004	0.111
sampleSizeContourPlots	0.067	0.003	0.071
sampleSizeParameters	69.992	10.626	82.493
sample_technicalVariance	17.509	2.430	21.329
spectrumFilter	5.923	1.184	7.535