BioC 3.3: CHECK report for SeqVarTools on morelia

Package: SeqVarTools

Version: 1.9.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqVarTools_1.9.16.tar.gz

StartedAt: 2016-04-21 07:29:35 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:33:21 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 225.1 seconds

RetCode: 0

Status:  OK

CheckDir: SeqVarTools.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 SeqVarTools_1.9.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SeqVarTools.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 ‘SeqVarTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqVarTools’ version ‘1.9.16’
* 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 ‘SeqVarTools’ can be installed ... [18s/19s] 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘SeqArray:::.altAllele’ ‘SeqArray:::.refAllele’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.runFirth: no visible global function definition for ‘as.formula’
.runFirth : <anonymous>: no visible global function definition for
  ‘model.matrix’
.runFirth: no visible global function definition for ‘coef’
.runFirth: no visible global function definition for ‘vcov’
.runFirth: no visible global function definition for ‘qchisq’
.runRegression: no visible global function definition for ‘as.formula’
.runRegression: no visible global function definition for ‘lm’
.runRegression: no visible global function definition for ‘glm’
.runRegression: no visible global function definition for ‘binomial’
.runRegression: no visible global function definition for ‘coef’
.runRegression: no visible global function definition for ‘vcov’
.waldTest: no visible global function definition for ‘pchisq’
refFracPlot,SeqVarGDSClass: no visible global function definition for
  ‘binom.test’
refFracPlot,SeqVarGDSClass: no visible global function definition for
  ‘plot’
refFracPlot,SeqVarGDSClass: no visible global function definition for
  ‘adjustcolor’
refFracPlot,SeqVarGDSClass: no visible global function definition for
  ‘abline’
refFracPlot,SeqVarGDSClass: no visible global function definition for
  ‘text’
regression,SeqVarData: no visible global function definition for
  ‘model.matrix’
regression,SeqVarData: no visible global function definition for
  ‘as.formula’
regression,SeqVarData : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  abline adjustcolor as.formula binom.test binomial coef glm lm
  model.matrix pchisq plot qchisq setNames text vcov
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "abline", "plot", "text")
  importFrom("stats", "as.formula", "binom.test", "binomial", "coef",
             "glm", "lm", "model.matrix", "pchisq", "qchisq", "setNames",
             "vcov")
to your NAMESPACE file.
* 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 ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [56s/56s]
 [57s/57s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/SeqVarTools.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqVarTools’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SeqVarTools)

name	user	system	elapsed
SeqVarData-class	0.113	0.004	0.207
allele-methods	0.015	0.001	0.015
alleleFrequency	0.129	0.014	0.144
alternateAlleleDetection	0.001	0.000	0.001
applyMethod	0.262	0.008	0.270
duplicateDiscordance	0.067	0.008	0.075
getGenotype	0.016	0.004	0.020
getVariableLengthData	0.010	0.003	0.029
heterozygosity	0.217	0.026	0.243
hwe	0.126	0.012	0.157
inbreedCoeff	0.217	0.017	0.234
isSNV	0.005	0.001	0.006
isVariant	0.006	0.001	0.007
meanBySample	0.025	0.003	0.049
mendelErr	0.047	0.005	0.052
missingGenotypeRate	0.025	0.001	0.026
pca	0.618	0.051	0.671
pedigree	0.004	0.001	0.006
refFrac	0.059	0.002	0.062
regression	0.121	0.004	0.125
setVariantID	0.012	0.003	0.015
titv	0.208	0.008	0.216