BioC 2.12: CHECK report for MEDIPS on petty

Package: MEDIPS

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.10.0.tar.gz

StartedAt: 2013-10-08 23:01:07 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:16:42 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 934.7 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 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' 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 'MEDIPS' can be installed ... [25s/25s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [6m/11m] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                149.309  4.730 228.546
MEDIPS.addCNV               66.833  2.711  70.003
MEDIPS.selectROIs           17.986  2.545  20.853
MEDIPS.plotSaturation       14.721  2.617  20.592
MEDIPS.saturation           15.194  1.527  17.383
MEDIPS.setAnnotation         6.260  0.672  10.905
MEDIPS.plotSeqCoverage       5.800  0.809   6.762
MEDIPS.seqCoverage           5.054  1.037   6.143
MEDIPS.plotCalibrationPlot   5.377  0.675  10.120
MEDIPS.selectSig             4.963  0.863   5.848
MEDIPS.getAnnotation         0.215  0.029 262.884
* 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 'MEDIPS' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MEDIPS)

name	user	system	elapsed
COUPLINGset-class	0.357	0.003	0.361
MEDIPS.CpGenrich	0.152	0.015	0.169
MEDIPS.addCNV	66.833	2.711	70.003
MEDIPS.annotate	0.003	0.003	0.006
MEDIPS.correlation	0.625	0.188	0.825
MEDIPS.couplingVector	3.574	0.477	4.059
MEDIPS.coverageAnalysis	0.003	0.006	0.008
MEDIPS.createROIset	1.367	0.301	1.674
MEDIPS.createSet	1.793	0.391	2.188
MEDIPS.exportWIG	2.597	0.463	3.072
MEDIPS.genomeVector	0.002	0.005	0.006
MEDIPS.getAnnotation	0.215	0.029	262.884
MEDIPS.mergeFrames	0.016	0.007	0.022
MEDIPS.mergeSets	0.508	0.031	1.086
MEDIPS.meth	149.309	4.730	228.546
MEDIPS.methylProfiling	0.003	0.005	0.007
MEDIPS.normalize	0.003	0.005	0.011
MEDIPS.plotCalibrationPlot	5.377	0.675	10.120
MEDIPS.plotCoverage	0.003	0.004	0.014
MEDIPS.plotSaturation	14.721	2.617	20.592
MEDIPS.plotSeqCoverage	5.800	0.809	6.762
MEDIPS.readAlignedSequences	0.002	0.003	0.006
MEDIPS.saturation	15.194	1.527	17.383
MEDIPS.saturationAnalysis	0.003	0.004	0.006
MEDIPS.selectROIs	17.986	2.545	20.853
MEDIPS.selectSig	4.963	0.863	5.848
MEDIPS.selectSignificants	0.002	0.004	0.007
MEDIPS.seqCoverage	5.054	1.037	6.143
MEDIPS.setAnnotation	6.260	0.672	10.905
MEDIPSroiSet-class	0.004	0.005	0.009
MEDIPSset-class	0.005	0.008	0.013