BioC 2.13: CHECK report for MEDIPS on perceval

Package: MEDIPS

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.12.0.tar.gz

StartedAt: 2014-04-05 02:29:08 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:38:42 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 574.5 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/MEDIPS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.12.0’
* 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BSgenome’ ‘DNAcopy’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘GenomicFeatures’ ‘GenomicRanges’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘MEDIPS.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [307s/340s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                110.762  4.250 125.332
MEDIPS.addCNV               63.785  3.141  75.162
MEDIPS.saturation           24.957  1.839  27.232
MEDIPS.selectROIs           22.500  2.842  25.839
MEDIPS.plotSaturation       16.594  4.143  21.073
MEDIPS.plotSeqCoverage       6.415  1.198   7.842
MEDIPS.seqCoverage           4.744  1.620   6.406
MEDIPS.setAnnotation         4.481  0.757   9.282
MEDIPS.plotCalibrationPlot   3.893  0.752   5.125
MEDIPS.getAnnotation         0.162  0.020   6.599
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/MEDIPS.Rcheck/00check.log’
for details.

* 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	0.011	0.002	0.013
MEDIPS.CpGenrich	0.161	0.011	0.183
MEDIPS.addCNV	63.785	3.141	75.162
MEDIPS.annotate	0.003	0.004	0.007
MEDIPS.correlation	0.639	0.211	0.945
MEDIPS.couplingVector	3.285	0.624	4.359
MEDIPS.coverageAnalysis	0.002	0.003	0.010
MEDIPS.createROIset	1.229	0.331	1.743
MEDIPS.createSet	1.569	0.470	2.179
MEDIPS.exportWIG	2.315	0.577	3.054
MEDIPS.genomeVector	0.003	0.005	0.007
MEDIPS.getAnnotation	0.162	0.020	6.599
MEDIPS.mergeFrames	0.030	0.021	0.052
MEDIPS.mergeSets	0.563	0.031	0.609
MEDIPS.meth	110.762	4.250	125.332
MEDIPS.methylProfiling	0.003	0.006	0.010
MEDIPS.normalize	0.002	0.004	0.008
MEDIPS.plotCalibrationPlot	3.893	0.752	5.125
MEDIPS.plotCoverage	0.003	0.005	0.008
MEDIPS.plotSaturation	16.594	4.143	21.073
MEDIPS.plotSeqCoverage	6.415	1.198	7.842
MEDIPS.readAlignedSequences	0.003	0.005	0.007
MEDIPS.saturation	24.957	1.839	27.232
MEDIPS.saturationAnalysis	0.003	0.005	0.008
MEDIPS.selectROIs	22.500	2.842	25.839
MEDIPS.selectSig	3.522	0.961	4.574
MEDIPS.selectSignificants	0.003	0.005	0.008
MEDIPS.seqCoverage	4.744	1.620	6.406
MEDIPS.setAnnotation	4.481	0.757	9.282
MEDIPSroiSet-class	0.004	0.008	0.012
MEDIPSset-class	0.005	0.010	0.014