BioC 3.5: CHECK report for cpvSNP on oaxaca

Package: cpvSNP

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cpvSNP_1.7.0.tar.gz

StartedAt: 2017-03-04 01:18:26 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:23:17 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 291.2 seconds

RetCode: 0

Status:  OK

CheckDir: cpvSNP.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 cpvSNP_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/cpvSNP.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 ‘cpvSNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cpvSNP’ version ‘1.7.0’
* 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 ‘cpvSNP’ 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' call to ‘GSEABase’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assocPvalBySetPlot: no visible global function definition for ‘rgb’
assocPvalBySetPlot: no visible global function definition for ‘col2rgb’
assocPvalBySetPlot : <anonymous>: no visible global function definition
  for ‘density’
assocPvalBySetPlot: no visible global function definition for ‘plot’
assocPvalBySetPlot: no visible global function definition for ‘legend’
assocPvalBySetPlot: no visible global function definition for ‘polygon’
assocPvalBySetPlot: no visible global function definition for ‘lines’
assocPvalBySetPlot: no visible global function definition for ‘points’
createArrayData: no visible global function definition for ‘GRanges’
createArrayData: no visible global function definition for ‘Rle’
createArrayData: no visible global function definition for ‘IRanges’
createArrayData: no visible global function definition for
  ‘elementMetadata<-’
geneToSNPList: no visible global function definition for ‘findOverlaps’
glossiMarginal: no visible global function definition for ‘pgamma’
plotPvals: no visible binding for global variable ‘df’
plotPvals: no visible binding for global variable ‘pval’
simulate_chisq: no visible global function definition for ‘rnorm’
vegasMarginal: no visible global function definition for ‘rbinom’
vegasMarginal: no visible global function definition for ‘qchisq’
vegasPrep: no visible global function definition for ‘elementMetadata’
show,VEGASResult: no visible global function definition for ‘var’
Undefined global functions or variables:
  GRanges IRanges Rle col2rgb density df elementMetadata
  elementMetadata<- findOverlaps legend lines pgamma plot points
  polygon pval qchisq rbinom rgb rnorm var
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "legend", "lines", "plot", "points", "polygon")
  importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom",
             "rnorm", "var")
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 ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
geneToSNPList 3.415  0.311   9.801
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.5-bioc/meat/cpvSNP.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GLOSSIResult-class	0.003	0.000	0.002
GLOSSIResultCollection-class	0.001	0.000	0.002
GeneSetResult-class	0.002	0.000	0.001
GeneSetResultCollection-class	0.001	0.001	0.001
VEGASResult-class	0.001	0.000	0.002
VEGASResultCollection-class	0.001	0.001	0.002
createArrayData	0.360	0.031	0.391
degreesOfFreedom-method	0.001	0.000	0.001
geneSetAnalysis	0.155	0.008	0.163
geneSetName-methods	0.001	0.000	0.001
geneToSNPList	3.415	0.311	9.801
glossi	0.008	0.024	0.032
glossiMarginal	0.003	0.002	0.005
pValue-method	0.001	0.000	0.001
simulatedStats-method	0.000	0.000	0.001
statistic-methods	0.001	0.000	0.000