BioC 3.3: CHECK report for methVisual on morelia

Package: methVisual

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methVisual_1.23.0.tar.gz

StartedAt: 2016-04-21 04:53:38 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:55:03 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 84.1 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.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 methVisual_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/methVisual.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methVisual/DESCRIPTION’ ... OK
* this is package ‘methVisual’ version ‘1.23.0’
* 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 ... [7s/7s] 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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
makeDataMethGFF: no visible binding for global variable ‘fn’
plotMatrixSNP: no visible global function definition for ‘color.legend’
Undefined global functions or variables:
  color.legend fn
* 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 files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	0.340	0.076	0.408
MethAlignNW	1.085	0.084	1.163
MethDataInput	0.023	0.007	0.030
MethLollipops	0.012	0.003	0.014
MethylQC	0.800	0.061	0.855
cgInAlign	0.002	0.002	0.003
cgMethFinder	0.001	0.000	0.001
coversionGenom	0.000	0.000	0.001
findNonAligned	0.003	0.002	0.006
heatMapMeth	0.065	0.008	0.072
makeDataMethGFF	0.109	0.009	0.118
makeLocalExpDir	0.021	0.006	0.028
makeTabFilePath	0.005	0.001	0.051
matrixSNP	0.196	0.063	0.251
methCA	0.014	0.003	0.017
methData	0.003	0.001	0.004
methFisherTest	0.033	0.004	0.037
methWhitneyUTest	0.005	0.002	0.007
plotAbsMethyl	0.004	0.002	0.006
plotMatrixSNP	0.429	0.125	0.537
readBisulfFASTA	0.058	0.009	0.067
selectRefSeq	0.014	0.006	0.020