BioC 3.0: CHECK report for metagene on oaxaca

Package: metagene

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metagene_1.0.0.tar.gz

StartedAt: 2015-04-10 01:07:01 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:11:35 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 274.4 seconds

RetCode: 0

Status:  OK

CheckDir: metagene.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 metagene_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/metagene.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagene/DESCRIPTION’ ... OK
* this is package ‘metagene’ version ‘1.0.0’
* 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 ‘metagene’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' calls in package code:
  ‘biomaRt’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
applyOnGroups: no visible global function definition for ‘mclapply’
bootstrapAnalysis: no visible global function definition for ‘mclapply’
getGenes: no visible binding for global variable ‘TSS.human’
getGenes: no visible binding for global variable ‘TSS.mouse’
getGenesBiomart: no visible global function definition for ‘useMart’
getGenesBiomart: no visible global function definition for ‘getBM’
parseBamFile: no visible global function definition for ‘ScanBamParam’
plotGraphic: no visible binding for global variable ‘distances’
plotGraphic: no visible binding for global variable ‘means’
plotGraphic: no visible binding for global variable ‘qinf’
plotGraphic: no visible binding for global variable ‘qsup’
plotGraphic: no visible binding for global variable ‘Groups’
prepareBamFiles : indexBamFiles: no visible global function definition
  for ‘sortBam’
prepareBamFiles : indexBamFiles: no visible global function definition
  for ‘indexBam’
prepareBamFiles : countAlignedReads: no visible global function
  definition for ‘countBam’
prepareBamFiles : countAlignedReads: no visible global function
  definition for ‘ScanBamParam’
prepareBamFiles : countAlignedReads: no visible global function
  definition for ‘scanBamFlag’
prepareBamFiles: no visible global function definition for ‘mclapply’
prepareFeatures: no visible global function definition for ‘mclapply’
scaleVectors : scaleBamFile: no visible global function definition for
  ‘mclapply’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
plotMatrices 10.123  0.226  10.404
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/20s]
 [20s/20s] 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/metagene.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
applyOnGroups	0.001	0.000	0.001
binBootstrap	0.001	0.000	0.001
binMatrix	0.001	0.000	0.000
bootstrapAnalysis	0.001	0.000	0.001
getDataFrame	0	0	0
getGenes	0.000	0.000	0.001
getGenesBiomart	0	0	0
mergeMatrix	0.001	0.000	0.001
parseBamFile	0.001	0.000	0.001
parseBamFiles	0.001	0.000	0.001
parseFeatures	1.829	0.030	1.867
parseRegions	1.545	0.028	1.594
plotGraphic	0.001	0.000	0.001
plotMatrices	10.123	0.226	10.404
prepareBamFiles	0.000	0.000	0.001
prepareFeatures	0.000	0.000	0.001
prepareRegions	0.000	0.000	0.001
rawCountsToRPM	0.000	0.000	0.001
removeControls	0.001	0.000	0.001
scaleVector	0	0	0
scaleVectors	0	0	0