BioC 2.12: CHECK report for clippda on george2

Package: clippda

Version: 1.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.10.0.tar.gz

StartedAt: 2013-10-09 00:57:35 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:07:39 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 603.8 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.10.0’
* 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 ... [6s/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 installed files from ‘inst/doc’ ... OK
* checking examples ... [471s/508s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          206.648  0.648 223.485
sampleSize               125.464  0.304 134.920
sampleSizeParameters      62.332  0.140  67.640
sample_technicalVariance  12.752  0.024  13.597
replicateCorrelations     10.545  0.012  11.436
betweensampleVariance      9.885  0.080  11.120
liverdata                  9.752  0.036  10.475
preProcRepeatedPeakData    8.541  0.008   9.275
spectrumFilter             7.865  0.004   8.563
* 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
** testing if installed package can be loaded
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.028	0.004	0.029
ZvaluesfrommultinomPlots	2.564	0.060	2.753
aclinicalProteomicsData-class	0.120	0.000	0.124
aclinicalProteomicsData-methods	0.480	0.232	0.717
betweensampleVariance	9.885	0.080	11.120
checkNo.replicates	0.968	0.020	1.043
clippda-package	206.648	0.648	223.485
f	0.020	0.004	0.024
fisherInformation	0.209	0.000	0.215
liverRawData	0.008	0.004	0.015
liver_pheno	0.016	0.000	0.017
liverdata	9.752	0.036	10.475
mostSimilarTwo	0.028	0.000	0.027
negativeIntensitiesCorrection	3.036	0.004	3.482
phenoDataFrame	0.164	0.000	0.204
pheno_urine	0.008	0.000	0.011
preProcRepeatedPeakData	8.541	0.008	9.275
proteomicsExprsData	0.388	0.004	0.471
proteomicspData	0.132	0.004	0.133
replicateCorrelations	10.545	0.012	11.436
sampleClusteredData	3.268	0.000	3.467
sampleSize	125.464	0.304	134.920
sampleSize3DscatterPlots	0.084	0.000	0.087
sampleSizeContourPlots	0.092	0.000	0.094
sampleSizeParameters	62.332	0.140	67.640
sample_technicalVariance	12.752	0.024	13.597
spectrumFilter	7.865	0.004	8.563
ztwo	0.012	0.000	0.012