BioC 2.12: CHECK report for clippda on petty

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: 2013-10-08 21:58:06 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:09:24 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 678.5 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 3.0.1 (2013-05-16)
* 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 ... [9s/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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'clippda.pdf' from 1615Kb to 341Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [572s/578s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          245.988 10.367 258.903
sampleSize               148.159  6.104 156.478
sampleSizeParameters      73.617  3.496  78.029
sample_technicalVariance  16.592  0.938  17.752
replicateCorrelations     13.237  0.573  13.915
liverdata                  9.935  0.303  10.292
betweensampleVariance      8.790  0.238   9.105
preProcRepeatedPeakData    8.495  0.275   8.799
spectrumFilter             8.375  0.192   8.636
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/clippda.Rcheck/00check.log'
for details.

* installing *source* package 'clippda' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  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, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.122	0.004	0.148
ZvaluesfrommultinomPlots	1.894	0.082	2.241
aclinicalProteomicsData-class	0.133	0.013	0.149
aclinicalProteomicsData-methods	0.470	0.362	0.839
betweensampleVariance	8.790	0.238	9.105
checkNo.replicates	0.743	0.041	0.789
clippda-package	245.988	10.367	258.903
f	0.006	0.009	0.015
fisherInformation	0.169	0.030	0.210
liverRawData	0.010	0.005	0.017
liver_pheno	0.004	0.004	0.007
liverdata	9.935	0.303	10.292
mostSimilarTwo	0.007	0.006	0.013
negativeIntensitiesCorrection	3.300	0.065	3.379
phenoDataFrame	0.123	0.025	0.148
pheno_urine	0.004	0.004	0.009
preProcRepeatedPeakData	8.495	0.275	8.799
proteomicsExprsData	0.507	0.036	0.544
proteomicspData	0.125	0.012	0.137
replicateCorrelations	13.237	0.573	13.915
sampleClusteredData	3.244	0.023	3.278
sampleSize	148.159	6.104	156.478
sampleSize3DscatterPlots	0.054	0.012	0.066
sampleSizeContourPlots	0.094	0.013	0.108
sampleSizeParameters	73.617	3.496	78.029
sample_technicalVariance	16.592	0.938	17.752
spectrumFilter	8.375	0.192	8.636
ztwo	0.005	0.008	0.014