BioC 2.14: CHECK report for MethylSeekR on petty

Package: MethylSeekR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MethylSeekR_1.4.0.tar.gz

StartedAt: 2014-10-07 22:51:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:08:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 974.7 seconds

RetCode: 0

Status:  OK

CheckDir: MethylSeekR.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 MethylSeekR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/MethylSeekR.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 ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.4.0’
* 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 ‘MethylSeekR’ can be installed ... [34s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘parallel’
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
Namespace in Imports field not imported from: ‘geneplotter’
  All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... [9m/11m] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
MethylSeekR-package         152.707  9.686 179.169
plotPMDSegmentation          96.104  5.861 105.941
segmentPMDs                  87.930  4.943 155.514
savePMDSegments              86.788  4.380  91.633
plotAlphaDistributionOneChr  17.083  0.653  18.881
calculateFDRs                14.379  1.892  25.252
plotFinalSegmentation        11.531  1.927  14.288
saveUMRLMRSegments            5.490  0.536   6.090
segmentUMRsLMRs               5.290  0.701  11.662
* 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/MethylSeekR.Rcheck/00check.log’
for details.

* installing *source* package ‘MethylSeekR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MethylSeekR)

name	user	system	elapsed
MethylSeekR-package	152.707	9.686	179.169
calculateFDRs	14.379	1.892	25.252
plotAlphaDistributionOneChr	17.083	0.653	18.881
plotFinalSegmentation	11.531	1.927	14.288
plotPMDSegmentation	96.104	5.861	105.941
readMethylome	1.268	0.120	1.415
readSNPTable	0.585	0.027	0.618
removeSNPs	1.912	0.151	2.107
savePMDSegments	86.788	4.380	91.633
saveUMRLMRSegments	5.490	0.536	6.090
segmentPMDs	87.930	4.943	155.514
segmentUMRsLMRs	5.290	0.701	11.662