BioC 2.13: CHECK report for MEDIPS on zin1

Package: MEDIPS

Version: 1.12.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.12.0.tar.gz

StartedAt: 2014-04-05 02:20:18 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:25:25 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 307.0 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MEDIPS.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... [13s/13s] 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 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 ... [168s/180s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           67.392  0.076  67.662
MEDIPS.addCNV         38.402  0.328  39.407
MEDIPS.saturation     12.489  0.012  12.523
MEDIPS.plotSaturation 10.969  0.024  11.029
MEDIPS.selectROIs      9.196  0.180   9.392
MEDIPS.setAnnotation   3.276  0.052   7.535
MEDIPS.getAnnotation   0.112  0.004   6.582
* 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
  ‘/home/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	0.004	0.000	0.005
MEDIPS.CpGenrich	0.072	0.012	0.084
MEDIPS.addCNV	38.402	0.328	39.407
MEDIPS.annotate	0.000	0.000	0.001
MEDIPS.correlation	0.336	0.044	0.388
MEDIPS.couplingVector	2.116	0.020	2.140
MEDIPS.coverageAnalysis	0.004	0.000	0.001
MEDIPS.createROIset	0.816	0.000	0.862
MEDIPS.createSet	1.057	0.004	1.060
MEDIPS.exportWIG	1.500	0.008	1.510
MEDIPS.genomeVector	0.004	0.000	0.001
MEDIPS.getAnnotation	0.112	0.004	6.582
MEDIPS.mergeFrames	0.012	0.000	0.014
MEDIPS.mergeSets	0.224	0.004	0.236
MEDIPS.meth	67.392	0.076	67.662
MEDIPS.methylProfiling	0.000	0.000	0.001
MEDIPS.normalize	0.000	0.000	0.001
MEDIPS.plotCalibrationPlot	3.080	0.028	3.113
MEDIPS.plotCoverage	0.000	0.000	0.001
MEDIPS.plotSaturation	10.969	0.024	11.029
MEDIPS.plotSeqCoverage	4.184	0.028	4.223
MEDIPS.readAlignedSequences	0.004	0.000	0.006
MEDIPS.saturation	12.489	0.012	12.523
MEDIPS.saturationAnalysis	0.000	0.000	0.001
MEDIPS.selectROIs	9.196	0.180	9.392
MEDIPS.selectSig	2.737	0.012	2.753
MEDIPS.selectSignificants	0.000	0.004	0.001
MEDIPS.seqCoverage	2.956	0.048	3.009
MEDIPS.setAnnotation	3.276	0.052	7.535
MEDIPSroiSet-class	0.004	0.000	0.002
MEDIPSset-class	0.004	0.000	0.002