Package: clippda

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.3.0.tar.gz

StartedAt: 2011-05-09 13:58:28 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:09:38 -0700 (Mon, 09 May 2011)

EllapsedTime: 670.8 seconds

RetCode: 0

Status:  OK

CheckDir: clippda.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/clippda.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.3.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file(s) in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 281Kb to 160Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* 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

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘clippda.Rnw’ 
** testing if installed package can be loaded

* DONE (clippda)

name	user	system	elapsed
aclinicalProteomicsData-class	0.120	0.012	0.139
aclinicalProteomicsData-methods	1.412	0.419	2.027
betweensampleVariance	6.728	1.024	8.464
checkNo.replicates	0.405	0.115	0.620
clippda-package	226.613	35.041	269.920
fisherInformation	0.159	0.013	0.186
liverRawData	0.033	0.003	0.035
liver_pheno	0.003	0.001	0.003
liverdata	7.022	1.351	8.789
mostSimilarTwo	0.005	0.000	0.005
negativeIntensitiesCorrection	2.370	0.286	2.733
phenoDataFrame	0.124	0.013	0.137
pheno_urine	0.003	0.001	0.003
preProcRepeatedPeakData	6.386	1.245	7.696
proteomicsExprsData	0.604	0.080	0.690
proteomicspData	0.129	0.014	0.159
replicateCorrelations	12.897	1.819	15.473
sampleClusteredData	2.341	0.265	2.784
sampleSize	142.446	20.987	166.839
sampleSize3DscatterPlots	0.139	0.004	0.142
sampleSizeContourPlots	0.065	0.003	0.073
sampleSizeParameters	69.513	10.657	82.971
sample_technicalVariance	17.236	2.433	20.212
spectrumFilter	5.830	1.181	7.149