Package: clippda

Version: 1.8.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.8.0.tar.gz

StartedAt: 2013-03-25 00:13:25 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:19:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 350.2 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/clippda.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.8.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          126.552  0.576 129.823
sampleSize                75.337  0.176  77.039
sampleSizeParameters      39.138  0.112  40.057
sample_technicalVariance   8.889  0.016   9.154
replicateCorrelations      6.376  0.024   6.530
liverdata                  4.884  0.004   5.036
* 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	0.012	0.000	0.011
ZvaluesfrommultinomPlots	1.652	0.032	1.725
aclinicalProteomicsData-class	0.208	0.004	0.250
aclinicalProteomicsData-methods	0.380	0.140	0.564
betweensampleVariance	4.324	0.068	4.596
checkNo.replicates	0.328	0.008	0.337
clippda-package	126.552	0.576	129.823
f	0.000	0.000	0.001
fisherInformation	0.100	0.004	0.105
liverRawData	0.004	0.000	0.005
liver_pheno	0.000	0.000	0.002
liverdata	4.884	0.004	5.036
mostSimilarTwo	0.004	0.000	0.002
negativeIntensitiesCorrection	1.524	0.004	1.532
phenoDataFrame	0.072	0.000	0.072
pheno_urine	0.000	0.000	0.002
preProcRepeatedPeakData	4.105	0.004	4.206
proteomicsExprsData	0.248	0.000	0.247
proteomicspData	0.212	0.000	0.210
replicateCorrelations	6.376	0.024	6.530
sampleClusteredData	1.664	0.000	1.707
sampleSize	75.337	0.176	77.039
sampleSize3DscatterPlots	0.136	0.004	0.140
sampleSizeContourPlots	0.036	0.000	0.038
sampleSizeParameters	39.138	0.112	40.057
sample_technicalVariance	8.889	0.016	9.154
spectrumFilter	4.184	0.000	4.247
ztwo	0	0	0