Package: clippda

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.8.0.tar.gz

StartedAt: 2013-03-24 23:01:49 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:09:58 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 488.6 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/clippda.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.8.0'
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          140.246 33.782 199.698
sampleSize                83.636 18.655 105.646
sampleSizeParameters      41.530  9.890  53.308
sample_technicalVariance   9.856  2.189  12.614
replicateCorrelations      7.519  1.553   9.653
liverdata                  4.780  1.493   6.461
spectrumFilter             3.951  1.208   5.495
betweensampleVariance      3.996  1.157   6.365
preProcRepeatedPeakData    3.953  1.166   5.206
* 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	0.013	0.004	0.021
ZvaluesfrommultinomPlots	1.313	0.201	1.711
aclinicalProteomicsData-class	0.076	0.013	0.109
aclinicalProteomicsData-methods	0.311	0.300	0.787
betweensampleVariance	3.996	1.157	6.365
checkNo.replicates	0.287	0.117	0.506
clippda-package	140.246	33.782	199.698
f	0	0	0
fisherInformation	0.089	0.012	0.101
liverRawData	0.006	0.002	0.007
liver_pheno	0.002	0.001	0.003
liverdata	4.780	1.493	6.461
mostSimilarTwo	0.003	0.001	0.002
negativeIntensitiesCorrection	1.543	0.315	2.017
phenoDataFrame	0.065	0.009	0.075
pheno_urine	0.002	0.001	0.002
preProcRepeatedPeakData	3.953	1.166	5.206
proteomicsExprsData	0.320	0.079	0.402
proteomicspData	0.066	0.011	0.078
replicateCorrelations	7.519	1.553	9.653
sampleClusteredData	1.515	0.272	1.855
sampleSize	83.636	18.655	105.646
sampleSize3DscatterPlots	0.027	0.009	0.038
sampleSizeContourPlots	0.045	0.006	0.052
sampleSizeParameters	41.530	9.890	53.308
sample_technicalVariance	9.856	2.189	12.614
spectrumFilter	3.951	1.208	5.495
ztwo	0	0	0