BioC 2.12: CHECK report for MEDIPS on pelham

Package: MEDIPS

Version: 1.9.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.9.4.tar.gz

StartedAt: 2013-03-24 07:27:14 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 07:36:17 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 543.0 seconds

RetCode: 0

Status: OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MEDIPS.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.9.4'
* 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 'MEDIPS' can be installed ... [23s/24s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [307s/321s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                121.998  4.806 128.534
MEDIPS.addCNV               65.776  3.007  70.069
MEDIPS.selectROIs           19.534  2.898  22.517
MEDIPS.plotSaturation       13.012  2.892  16.015
MEDIPS.saturation           14.163  1.675  15.898
MEDIPS.plotSeqCoverage       6.613  1.030   7.663
MEDIPS.setAnnotation         6.548  0.851  10.730
MEDIPS.plotCalibrationPlot   5.783  0.739   6.623
MEDIPS.seqCoverage           4.953  1.192   6.155
MEDIPS.selectSig             5.084  1.009   6.116
MEDIPS.getAnnotation         0.158  0.016   6.825
* 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 'MEDIPS' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MEDIPS.Rnw' 
** testing if installed package can be loaded
* DONE (MEDIPS)

name	user	system	elapsed
COUPLINGset-class	0.007	0.003	0.010
MEDIPS.CpGenrich	0.123	0.012	0.136
MEDIPS.addCNV	65.776	3.007	70.069
MEDIPS.annotate	0.003	0.004	0.007
MEDIPS.correlation	0.577	0.206	0.975
MEDIPS.couplingVector	3.364	0.511	4.161
MEDIPS.coverageAnalysis	0.003	0.005	0.007
MEDIPS.createROIset	1.317	0.362	1.714
MEDIPS.createSet	1.775	0.462	2.254
MEDIPS.exportWIG	2.564	0.567	3.152
MEDIPS.genomeVector	0.004	0.008	0.012
MEDIPS.getAnnotation	0.158	0.016	6.825
MEDIPS.mergeFrames	0.011	0.006	0.018
MEDIPS.mergeSets	0.428	0.023	0.464
MEDIPS.meth	121.998	4.806	128.534
MEDIPS.methylProfiling	0.004	0.006	0.009
MEDIPS.normalize	0.003	0.006	0.010
MEDIPS.plotCalibrationPlot	5.783	0.739	6.623
MEDIPS.plotCoverage	0.004	0.006	0.009
MEDIPS.plotSaturation	13.012	2.892	16.015
MEDIPS.plotSeqCoverage	6.613	1.030	7.663
MEDIPS.readAlignedSequences	0.003	0.005	0.008
MEDIPS.saturation	14.163	1.675	15.898
MEDIPS.saturationAnalysis	0.003	0.005	0.008
MEDIPS.selectROIs	19.534	2.898	22.517
MEDIPS.selectSig	5.084	1.009	6.116
MEDIPS.selectSignificants	0.003	0.004	0.008
MEDIPS.seqCoverage	4.953	1.192	6.155
MEDIPS.setAnnotation	6.548	0.851	10.730
MEDIPSroiSet-class	0.004	0.009	0.014
MEDIPSset-class	0.005	0.014	0.019

Summary

Command output