BioC 2.12: CHECK report for MEDIPS on george2

Package: MEDIPS

Version: 1.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.10.0.tar.gz

StartedAt: 2013-10-09 03:07:12 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 03:18:18 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 666.5 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 3.0.1 (2013-05-16)
* 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 ‘1.10.0’
* 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 ... [27s/28s] 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 ... [381s/397s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                155.762  0.280 158.159
MEDIPS.addCNV              102.175  1.380 104.019
MEDIPS.selectROIs           30.346  0.548  31.124
MEDIPS.saturation           19.389  0.028  19.453
MEDIPS.plotSaturation       15.037  0.048  15.096
MEDIPS.plotSeqCoverage       7.244  0.104   8.046
MEDIPS.setAnnotation         5.944  0.140  10.049
MEDIPS.seqCoverage           5.705  0.260   6.004
MEDIPS.plotCalibrationPlot   5.605  0.084   5.691
MEDIPS.getAnnotation         0.200  0.008   8.487
* 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	0.464	0.000	0.462
MEDIPS.CpGenrich	0.088	0.016	0.105
MEDIPS.addCNV	102.175	1.380	104.019
MEDIPS.annotate	0.004	0.000	0.005
MEDIPS.correlation	1.044	0.100	1.250
MEDIPS.couplingVector	4.480	0.040	4.563
MEDIPS.coverageAnalysis	0.008	0.000	0.008
MEDIPS.createROIset	1.700	0.024	1.812
MEDIPS.createSet	2.228	0.024	2.255
MEDIPS.exportWIG	3.320	0.036	3.364
MEDIPS.genomeVector	0.008	0.000	0.008
MEDIPS.getAnnotation	0.200	0.008	8.487
MEDIPS.mergeFrames	0.020	0.000	0.017
MEDIPS.mergeSets	0.676	0.000	0.694
MEDIPS.meth	155.762	0.280	158.159
MEDIPS.methylProfiling	0.004	0.000	0.006
MEDIPS.normalize	0.004	0.000	0.005
MEDIPS.plotCalibrationPlot	5.605	0.084	5.691
MEDIPS.plotCoverage	0.012	0.000	0.009
MEDIPS.plotSaturation	15.037	0.048	15.096
MEDIPS.plotSeqCoverage	7.244	0.104	8.046
MEDIPS.readAlignedSequences	0.008	0.000	0.008
MEDIPS.saturation	19.389	0.028	19.453
MEDIPS.saturationAnalysis	0.004	0.000	0.007
MEDIPS.selectROIs	30.346	0.548	31.124
MEDIPS.selectSig	4.456	0.048	4.526
MEDIPS.selectSignificants	0.004	0.000	0.005
MEDIPS.seqCoverage	5.705	0.260	6.004
MEDIPS.setAnnotation	5.944	0.140	10.049
MEDIPSroiSet-class	0.000	0.012	0.013
MEDIPSset-class	0.000	0.020	0.018