BioC 3.0: CHECK report for methVisual on perceval

Package: methVisual

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.18.0.tar.gz

StartedAt: 2015-04-10 03:31:01 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:34:12 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 191.2 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 --no-multiarch methVisual_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/methVisual.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.0’
* 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 ... [17s/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 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’
* 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 ... [15s/15s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.523	0.143	0.642
MethAlignNW	1.887	0.161	2.067
MethDataInput	0.052	0.020	0.095
MethLollipops	0.014	0.003	0.016
MethylQC	1.322	0.128	1.467
cgInAlign	0.003	0.001	0.004
cgMethFinder	0.001	0.000	0.001
coversionGenom	0.001	0.000	0.001
findNonAligned	0.004	0.002	0.006
heatMapMeth	0.091	0.013	0.112
makeDataMethGFF	0.218	0.021	0.235
makeLocalExpDir	0.039	0.016	0.055
makeTabFilePath	0.013	0.004	0.154
matrixSNP	0.293	0.110	0.378
methCA	0.018	0.005	0.032
methData	0.002	0.001	0.003
methFisherTest	0.039	0.006	0.048
methWhitneyUTest	0.006	0.002	0.007
plotAbsMethyl	0.006	0.002	0.013
plotMatrixSNP	0.689	0.226	0.889
readBisulfFASTA	0.044	0.016	0.061
selectRefSeq	0.039	0.016	0.057