BioC 2.12: CHECK report for MEDIPS on pelham

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: 2013-05-01 07:48:08 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:57:13 -0700 (Wed, 01 May 2013)

EllapsedTime: 544.7 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 3.0.0 Patched (2013-04-08 r62531)
* 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 ... [22s/22s] 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 ... [310s/328s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                118.210  5.065 127.110
MEDIPS.addCNV               66.292  3.212  71.329
MEDIPS.selectROIs           19.603  2.919  22.880
MEDIPS.plotSaturation       14.816  3.072  18.222
MEDIPS.saturation           14.878  2.002  17.170
MEDIPS.plotSeqCoverage       7.205  1.061   8.428
MEDIPS.seqCoverage           6.177  1.245   7.521
MEDIPS.setAnnotation         6.188  0.830  11.412
MEDIPS.plotCalibrationPlot   5.408  0.745   6.302
MEDIPS.selectSig             5.064  1.001   6.116
MEDIPS.getAnnotation         0.156  0.016   6.145
* 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	0.319	0.004	0.329
MEDIPS.CpGenrich	0.138	0.014	0.152
MEDIPS.addCNV	66.292	3.212	71.329
MEDIPS.annotate	0.003	0.004	0.006
MEDIPS.correlation	0.605	0.207	0.871
MEDIPS.couplingVector	4.143	0.540	4.753
MEDIPS.coverageAnalysis	0.002	0.005	0.006
MEDIPS.createROIset	1.402	0.341	1.840
MEDIPS.createSet	1.985	0.464	2.495
MEDIPS.exportWIG	2.786	0.572	3.426
MEDIPS.genomeVector	0.002	0.004	0.007
MEDIPS.getAnnotation	0.156	0.016	6.145
MEDIPS.mergeFrames	0.011	0.007	0.018
MEDIPS.mergeSets	0.453	0.026	0.541
MEDIPS.meth	118.210	5.065	127.110
MEDIPS.methylProfiling	0.003	0.005	0.008
MEDIPS.normalize	0.003	0.005	0.009
MEDIPS.plotCalibrationPlot	5.408	0.745	6.302
MEDIPS.plotCoverage	0.003	0.005	0.009
MEDIPS.plotSaturation	14.816	3.072	18.222
MEDIPS.plotSeqCoverage	7.205	1.061	8.428
MEDIPS.readAlignedSequences	0.002	0.004	0.007
MEDIPS.saturation	14.878	2.002	17.170
MEDIPS.saturationAnalysis	0.003	0.004	0.008
MEDIPS.selectROIs	19.603	2.919	22.880
MEDIPS.selectSig	5.064	1.001	6.116
MEDIPS.selectSignificants	0.003	0.006	0.011
MEDIPS.seqCoverage	6.177	1.245	7.521
MEDIPS.setAnnotation	6.188	0.830	11.412
MEDIPSroiSet-class	0.004	0.007	0.011
MEDIPSset-class	0.005	0.009	0.014

Summary

Command output