BioC 2.14: CHECK report for MEDIPS on petty

Package: MEDIPS

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.14.0.tar.gz

StartedAt: 2014-10-07 22:49:02 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:00:09 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 667.4 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MEDIPS_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MEDIPS.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.14.0’
* 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 ... [31s/33s] 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... [308s/334s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
MEDIPS.meth                133.060  1.598 141.931
MEDIPS.addCNV               54.163  1.688  56.228
MEDIPS.saturation           20.059  0.904  21.770
MEDIPS.plotSaturation       19.283  1.457  22.071
MEDIPS.selectSig             9.072  0.411   9.541
MEDIPS.plotSeqCoverage       8.290  0.698   9.484
MEDIPS.selectROIs            7.828  0.285   8.186
MEDIPS.setAnnotation         7.452  0.540  15.090
MEDIPS.seqCoverage           5.902  0.866   6.784
MEDIPS.plotCalibrationPlot   5.343  0.572   6.247
MEDIPS.getAnnotation         0.217  0.011   7.789
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.003	0.000	0.004
MEDIPS.CpGenrich	0.570	0.014	0.585
MEDIPS.addCNV	54.163	1.688	56.228
MEDIPS.annotate	0.001	0.000	0.001
MEDIPS.correlation	0.656	0.096	0.778
MEDIPS.couplingVector	3.906	0.365	4.283
MEDIPS.coverageAnalysis	0.001	0.000	0.001
MEDIPS.createROIset	1.366	0.177	1.682
MEDIPS.createSet	1.845	0.248	2.150
MEDIPS.exportWIG	2.841	0.328	3.227
MEDIPS.genomeVector	0.001	0.000	0.002
MEDIPS.getAnnotation	0.217	0.011	7.789
MEDIPS.mergeFrames	0.011	0.000	0.011
MEDIPS.mergeSets	0.494	0.015	0.533
MEDIPS.meth	133.060	1.598	141.931
MEDIPS.methylProfiling	0.001	0.001	0.002
MEDIPS.normalize	0.002	0.000	0.001
MEDIPS.plotCalibrationPlot	5.343	0.572	6.247
MEDIPS.plotCoverage	0.001	0.000	0.001
MEDIPS.plotSaturation	19.283	1.457	22.071
MEDIPS.plotSeqCoverage	8.290	0.698	9.484
MEDIPS.readAlignedSequences	0.001	0.001	0.001
MEDIPS.saturation	20.059	0.904	21.770
MEDIPS.saturationAnalysis	0.001	0.000	0.001
MEDIPS.selectROIs	7.828	0.285	8.186
MEDIPS.selectSig	9.072	0.411	9.541
MEDIPS.selectSignificants	0.002	0.000	0.001
MEDIPS.seqCoverage	5.902	0.866	6.784
MEDIPS.setAnnotation	7.452	0.540	15.090
MEDIPSroiSet-class	0.002	0.000	0.003
MEDIPSset-class	0.003	0.000	0.004