BioC 2.14: CHECK report for MEDIPS on zin2

Package: MEDIPS

Version: 1.14.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.14.0.tar.gz

StartedAt: 2014-10-08 00:53:57 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:59:11 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 313.7 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/MEDIPS.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.14.0’
* 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 ... [14s/14s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [149s/167s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
MEDIPS.meth           61.952  0.020  62.201
MEDIPS.addCNV         31.858  0.200  32.147
MEDIPS.saturation      9.601  0.016   9.659
MEDIPS.plotSaturation  9.065  0.016   9.101
MEDIPS.setAnnotation   3.884  0.040  14.556
MEDIPS.getAnnotation   0.100  0.008   6.289
* 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
  ‘/home/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	0.004	0.000	0.001
MEDIPS.CpGenrich	0.064	0.012	0.075
MEDIPS.addCNV	31.858	0.200	32.147
MEDIPS.annotate	0.000	0.000	0.001
MEDIPS.correlation	0.340	0.016	0.364
MEDIPS.couplingVector	2.168	0.000	2.173
MEDIPS.coverageAnalysis	0	0	0
MEDIPS.createROIset	0.708	0.004	0.711
MEDIPS.createSet	0.932	0.008	0.943
MEDIPS.exportWIG	1.500	0.004	1.506
MEDIPS.genomeVector	0.000	0.000	0.001
MEDIPS.getAnnotation	0.100	0.008	6.289
MEDIPS.mergeFrames	0.008	0.000	0.006
MEDIPS.mergeSets	0.244	0.004	0.260
MEDIPS.meth	61.952	0.020	62.201
MEDIPS.methylProfiling	0.000	0.000	0.001
MEDIPS.normalize	0.000	0.000	0.001
MEDIPS.plotCalibrationPlot	3.164	0.024	3.229
MEDIPS.plotCoverage	0.004	0.000	0.001
MEDIPS.plotSaturation	9.065	0.016	9.101
MEDIPS.plotSeqCoverage	4.564	0.016	4.604
MEDIPS.readAlignedSequences	0.000	0.000	0.001
MEDIPS.saturation	9.601	0.016	9.659
MEDIPS.saturationAnalysis	0	0	0
MEDIPS.selectROIs	4.036	0.028	4.069
MEDIPS.selectSig	4.832	0.020	4.870
MEDIPS.selectSignificants	0.000	0.000	0.001
MEDIPS.seqCoverage	3.077	0.020	3.100
MEDIPS.setAnnotation	3.884	0.040	14.556
MEDIPSroiSet-class	0.000	0.000	0.001
MEDIPSset-class	0.004	0.000	0.001