BioC 2.13: CHECK report for methVisual on perceval

Package: methVisual

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.14.0.tar.gz

StartedAt: 2014-04-05 02:32:31 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:35:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 197.6 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/methVisual.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 ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ 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 ‘methVisual’ can be installed ... [15s/18s] 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:
  ‘Biostrings’ ‘grid’
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
Packages in Depends field not imported from:
  ‘gsubfn’ ‘plotrix’ ‘sqldf’
  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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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’:
  ‘methVisual.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [15s/21s] OK
* 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/methVisual.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Cooccurrence	0.565	0.135	1.224
MethAlignNW	2.108	0.187	3.457
MethDataInput	0.067	0.022	0.117
MethLollipops	0.019	0.002	0.021
MethylQC	1.607	0.148	2.585
cgInAlign	0.011	0.002	0.012
cgMethFinder	0.009	0.001	0.010
coversionGenom	0.007	0.000	0.010
findNonAligned	0.012	0.002	0.014
heatMapMeth	0.102	0.013	0.184
makeDataMethGFF	0.243	0.027	0.521
makeLocalExpDir	0.365	0.021	0.460
makeTabFilePath	0.027	0.007	0.208
matrixSNP	0.367	0.116	1.155
methCA	0.030	0.007	0.095
methData	0.010	0.001	0.012
methFisherTest	0.040	0.005	0.045
methWhitneyUTest	0.016	0.002	0.018
plotAbsMethyl	0.017	0.003	0.027
plotMatrixSNP	0.728	0.197	1.561
readBisulfFASTA	0.080	0.027	0.236
selectRefSeq	0.063	0.022	0.172