Package: MEDIPS

Version: 1.9.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.9.5.tar.gz

StartedAt: 2013-03-25 02:57:10 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:08:47 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 697.7 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/MEDIPS.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEDIPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEDIPS’ version ‘1.9.5’
* 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 ... [31s/31s] 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 ... [376s/400s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                157.154  0.368 163.570
MEDIPS.addCNV               96.854  1.372 100.584
MEDIPS.selectROIs           28.806  0.400  29.811
MEDIPS.saturation           18.813  0.028  19.248
MEDIPS.plotSaturation       15.153  0.052  15.311
MEDIPS.plotSeqCoverage       7.629  0.052   8.084
MEDIPS.setAnnotation         5.873  0.156   9.249
MEDIPS.seqCoverage           5.392  0.300   6.211
MEDIPS.plotCalibrationPlot   5.564  0.076   5.767
MEDIPS.getAnnotation         0.228  0.004   7.477
* 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	0.008	0.008	0.018
MEDIPS.CpGenrich	0.132	0.016	0.156
MEDIPS.addCNV	96.854	1.372	100.584
MEDIPS.annotate	0.004	0.004	0.008
MEDIPS.correlation	0.968	0.132	1.237
MEDIPS.couplingVector	4.077	0.048	4.774
MEDIPS.coverageAnalysis	0.008	0.000	0.008
MEDIPS.createROIset	1.716	0.020	1.763
MEDIPS.createSet	2.224	0.016	2.256
MEDIPS.exportWIG	2.804	0.016	2.853
MEDIPS.genomeVector	0.008	0.000	0.009
MEDIPS.getAnnotation	0.228	0.004	7.477
MEDIPS.mergeFrames	0.024	0.000	0.021
MEDIPS.mergeSets	0.664	0.008	0.698
MEDIPS.meth	157.154	0.368	163.570
MEDIPS.methylProfiling	0.008	0.000	0.008
MEDIPS.normalize	0.008	0.000	0.007
MEDIPS.plotCalibrationPlot	5.564	0.076	5.767
MEDIPS.plotCoverage	0.008	0.000	0.007
MEDIPS.plotSaturation	15.153	0.052	15.311
MEDIPS.plotSeqCoverage	7.629	0.052	8.084
MEDIPS.readAlignedSequences	0.008	0.000	0.011
MEDIPS.saturation	18.813	0.028	19.248
MEDIPS.saturationAnalysis	0.008	0.000	0.007
MEDIPS.selectROIs	28.806	0.400	29.811
MEDIPS.selectSig	4.456	0.032	4.513
MEDIPS.selectSignificants	0.008	0.000	0.007
MEDIPS.seqCoverage	5.392	0.300	6.211
MEDIPS.setAnnotation	5.873	0.156	9.249
MEDIPSroiSet-class	0.016	0.000	0.014
MEDIPSset-class	0.016	0.004	0.018