BioC 3.5: CHECK report for RSVSim on oaxaca

Package: RSVSim

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RSVSim_1.15.0.tar.gz

StartedAt: 2017-03-04 08:35:30 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:38:35 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 185.3 seconds

RetCode: 0

Status:  OK

CheckDir: RSVSim.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 RSVSim_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RSVSim.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RSVSim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RSVSim’ version ‘1.15.0’
* 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 ‘RSVSim’ can be installed ... 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:
  ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Hsapiens.UCSC.hg19.masked’
  ‘MASS’ ‘rtracklayer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.drawPos: no visible global function definition for ‘seqlevels’
.drawPos: no visible global function definition for ‘queryHits’
.getHG19: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
.getHG19: no visible binding for global variable ‘Hsapiens’
.getHG19: no visible global function definition for ‘as’
.getSVSizes: no visible global function definition for ‘rbeta’
.loadFromBSGenome_TandemRepeats: no visible binding for global variable
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
.loadFromBSGenome_TandemRepeats: no visible global function definition
  for ‘seqlevels<-’
.loadFromBSGenome_TandemRepeats: no visible global function definition
  for ‘as’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘browserSession’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘genome<-’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘ucscTableQuery’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘txtProgressBar’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘range<-’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘getTable’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘setTxtProgressBar’
.loadFromUCSC_RepeatMasks: no visible global function definition for
  ‘data’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘browserSession’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘genome<-’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘getTable’
.loadFromUCSC_SegDups: no visible global function definition for
  ‘ucscTableQuery’
.readRepeatMaskerOutput: no visible global function definition for
  ‘read.table’
.readRepeatMaskerOutput: no visible global function definition for
  ‘data’
.simInsertionPositions: no visible global function definition for
  ‘txtProgressBar’
.simInsertionPositions: no visible global function definition for
  ‘seqlevels’
.simInsertionPositions: no visible global function definition for
  ‘setTxtProgressBar’
.simPositions: no visible global function definition for
  ‘txtProgressBar’
.simPositions: no visible global function definition for
  ‘setTxtProgressBar’
.simTranslocationPositions: no visible global function definition for
  ‘txtProgressBar’
.simTranslocationPositions: no visible global function definition for
  ‘seqlevels’
.simTranslocationPositions: no visible global function definition for
  ‘setTxtProgressBar’
.subtractIntervals: no visible global function definition for
  ‘seqlevels<-’
.testSVSim: no visible global function definition for ‘metadata’
compareSV,character-character: no visible global function definition
  for ‘read.table’
compareSV,character-data.frame: no visible global function definition
  for ‘read.table’
estimateSVSizes,numeric-numeric-ANY-ANY-missing: no visible global
  function definition for ‘fitdistr’
simulateSV,ANY: no visible global function definition for ‘data’
simulateSV,ANY: no visible global function definition for
  ‘txtProgressBar’
simulateSV,ANY: no visible global function definition for
  ‘setTxtProgressBar’
simulateSV,ANY: no visible global function definition for ‘write.table’
simulateSV,ANY: no visible global function definition for ‘metadata<-’
Undefined global functions or variables:
  BSgenome.Hsapiens.UCSC.hg19.masked Hsapiens as browserSession data
  fitdistr genome<- getTable metadata metadata<- queryHits range<-
  rbeta read.table seqlevels seqlevels<- setTxtProgressBar
  txtProgressBar ucscTableQuery write.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbeta")
  importFrom("utils", "data", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
simulateSV 5.917  0.032   5.949
compareSVs 5.774  0.020   5.797
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RSVSim.Rcheck/00check.log’
for details.

* installing *source* package ‘RSVSim’ ...
** 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 (RSVSim)

name	user	system	elapsed
compareSVs	5.774	0.020	5.797
estimateSVSizes	0.597	0.010	0.607
segmentalDuplications	0.101	0.007	0.107
simulateSV	5.917	0.032	5.949
weightsMechanisms	0.002	0.000	0.003
weightsRepeats	0.003	0.000	0.004