Package: clippda

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.10.0.tar.gz

StartedAt: 2013-05-01 03:50:33 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:01:32 -0700 (Wed, 01 May 2013)

EllapsedTime: 659.0 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [7s/9s] 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 ... [557s/568s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          236.501 14.311 254.334
sampleSize               141.272  8.424 154.590
sampleSizeParameters      70.143  4.535  76.300
sample_technicalVariance  14.930  1.153  16.457
replicateCorrelations     11.809  0.720  12.670
liverdata                  9.888  0.338  10.370
betweensampleVariance      9.780  0.223  10.088
spectrumFilter             8.521  0.286   8.935
preProcRepeatedPeakData    8.367  0.328   8.884
* 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
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.122	0.003	0.126
ZvaluesfrommultinomPlots	1.898	0.084	2.029
aclinicalProteomicsData-class	0.111	0.015	0.127
aclinicalProteomicsData-methods	0.354	0.418	0.778
betweensampleVariance	9.780	0.223	10.088
checkNo.replicates	0.957	0.067	1.029
clippda-package	236.501	14.311	254.334
f	0.011	0.012	0.023
fisherInformation	0.140	0.033	0.177
liverRawData	0.009	0.005	0.014
liver_pheno	0.004	0.003	0.006
liverdata	9.888	0.338	10.370
mostSimilarTwo	0.012	0.005	0.018
negativeIntensitiesCorrection	3.199	0.080	3.308
phenoDataFrame	0.109	0.021	0.137
pheno_urine	0.009	0.006	0.015
preProcRepeatedPeakData	8.367	0.328	8.884
proteomicsExprsData	0.402	0.033	0.443
proteomicspData	0.105	0.020	0.127
replicateCorrelations	11.809	0.720	12.670
sampleClusteredData	3.296	0.082	3.402
sampleSize	141.272	8.424	154.590
sampleSize3DscatterPlots	0.054	0.018	0.072
sampleSizeContourPlots	0.082	0.019	0.109
sampleSizeParameters	70.143	4.535	76.300
sample_technicalVariance	14.930	1.153	16.457
spectrumFilter	8.521	0.286	8.935
ztwo	0.007	0.010	0.016