BioC 3.4: CHECK report for supraHex on morelia

Package: supraHex

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings supraHex_1.11.1.tar.gz

StartedAt: 2016-09-20 13:40:13 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:40:53 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 40.6 seconds

RetCode: 0

Status:  OK

CheckDir: supraHex.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 supraHex_1.11.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/supraHex.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘supraHex/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘supraHex’ version ‘1.11.1’
* 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 ‘supraHex’ 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sDistance: no visible global function definition for ‘cor’
sDmat: no visible global function definition for ‘median’
sDmatCluster: no visible global function definition for ‘as.dist’
sDmatCluster: no visible global function definition for ‘hclust’
sInitial: no visible global function definition for ‘runif’
sTrainSeq: no visible global function definition for ‘runif’
sWriteData: no visible global function definition for ‘write.table’
visColoralpha: no visible global function definition for ‘rgb2hsv’
visColoralpha: no visible global function definition for ‘col2rgb’
visColoralpha: no visible global function definition for ‘hsv’
visColormap: no visible global function definition for
  ‘colorRampPalette’
visCompReorder: no visible global function definition for ‘quantile’
visDmatCluster: no visible global function definition for ‘dev.new’
visDmatHeatmap: no visible global function definition for ‘as.dist’
visDmatHeatmap: no visible global function definition for ‘hclust’
visDmatHeatmap: no visible global function definition for ‘abline’
visDmatHeatmap: no visible global function definition for ‘legend’
visHeatmap: no visible global function definition for ‘as.dist’
visHeatmap: no visible global function definition for ‘hclust’
visHeatmap: no visible global function definition for ‘as.dendrogram’
visHeatmap: no visible global function definition for ‘cutree’
visHeatmap: no visible global function definition for ‘quantile’
visHeatmap: no visible global function definition for ‘heatmap’
visHeatmapAdv: no visible global function definition for ‘as.dist’
visHeatmapAdv: no visible global function definition for ‘hclust’
visHeatmapAdv: no visible global function definition for ‘cutree’
visHeatmapAdv: no visible global function definition for ‘quantile’
visHeatmapAdv : heatmap.2: no visible binding for global variable
  ‘dist’
visHeatmapAdv : heatmap.2: no visible binding for global variable
  ‘hclust’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘par’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘median’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘order.dendrogram’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘as.dendrogram’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘reorder’
visHeatmapAdv : heatmap.2: no visible binding for global variable ‘sd’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘layout’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘image’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘box’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘abline’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘axis’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘text’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘strheight’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘mtext’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘strwidth’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘rect’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘lines’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘plot.new’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘title’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘density’
visHeatmapAdv : heatmap.2: no visible global function definition for
  ‘hist’
visHeatmapAdv : <anonymous>: no visible global function definition for
  ‘as.dist’
visHeatmapAdv : <anonymous>: no visible global function definition for
  ‘hclust’
visHexBarplot: no visible global function definition for ‘dev.new’
visHexBarplot: no visible global function definition for ‘par’
visHexBarplot: no visible global function definition for ‘lines’
visHexBarplot: no visible global function definition for ‘rect’
visHexBarplot: no visible global function definition for ‘text’
visHexMapping: no visible global function definition for ‘dev.new’
visHexMapping: no visible global function definition for ‘rainbow’
visHexMulComp: no visible global function definition for ‘quantile’
visHexPattern: no visible global function definition for ‘dev.new’
visHexPattern: no visible global function definition for ‘par’
visHexPattern: no visible global function definition for ‘symbols’
visHexPattern: no visible global function definition for ‘stars’
visHexPattern: no visible global function definition for ‘lines’
visHexPattern: no visible global function definition for ‘points’
visHexPattern: no visible global function definition for ‘rect’
visKernels: no visible global function definition for ‘dev.new’
visKernels: no visible global function definition for ‘par’
visKernels: no visible global function definition for ‘rainbow’
visKernels: no visible global function definition for ‘lines’
visKernels: no visible global function definition for ‘legend’
visTreeBootstrap: no visible global function definition for ‘as.dist’
visTreeBootstrap : f: no visible global function definition for
  ‘as.dist’
visTreeBootstrap: no visible global function definition for ‘abline’
visVp: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.dendrogram as.dist axis box col2rgb colorRampPalette cor
  cutree density dev.new dist hclust heatmap hist hsv image layout
  legend lines median mtext order.dendrogram par plot.new points
  quantile rainbow rect reorder rgb2hsv runif sd stars strheight
  strwidth symbols text title write.table
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.new",
             "hsv", "rainbow", "rgb2hsv")
  importFrom("graphics", "abline", "axis", "box", "hist", "image",
             "layout", "legend", "lines", "mtext", "par", "plot.new",
             "points", "rect", "stars", "strheight", "strwidth",
             "symbols", "text", "title")
  importFrom("stats", "as.dendrogram", "as.dist", "cor", "cutree",
             "density", "dist", "hclust", "heatmap", "median",
             "order.dendrogram", "quantile", "reorder", "runif", "sd")
  importFrom("utils", "write.table")
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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/supraHex.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
sBMH	0.056	0.004	0.060
sCompReorder	0.617	0.008	0.625
sDistance	0.081	0.003	0.084
sDmat	0.155	0.005	0.160
sDmatCluster	0.228	0.008	0.236
sDmatMinima	0.093	0.003	0.096
sHexDist	0.003	0.000	0.003
sHexGrid	0.002	0.000	0.002
sInitial	0.002	0.001	0.002
sMapOverlay	0.151	0.006	0.158
sNeighAny	0.005	0.001	0.005
sNeighDirect	0.003	0.000	0.003
sPipeline	0.287	0.008	0.296
sTopology	0.014	0.003	0.018
sTrainBatch	0.037	0.001	0.039
sTrainSeq	0.347	0.002	0.349
sTrainology	0.005	0.000	0.005
sWriteData	0.244	0.005	0.249
visColoralpha	0.004	0.000	0.004
visColorbar	0.032	0.001	0.033
visColormap	0.004	0.001	0.004
visCompReorder	1.037	0.038	1.077
visDmatCluster	0.283	0.029	0.313
visDmatHeatmap	0.196	0.005	0.202
visHeatmap	0.078	0.001	0.079
visHeatmapAdv	0.384	0.004	0.389
visHexAnimate	0.001	0.000	0.001
visHexBarplot	0.658	0.020	0.678
visHexComp	0.087	0.004	0.092
visHexGrid	0.082	0.003	0.085
visHexMapping	0.942	0.057	1.000
visHexMulComp	0.638	0.025	0.663
visHexPattern	1.393	0.088	1.483
visKernels	0.012	0.006	0.019
visTreeBSclust	0.071	0.004	0.075
visTreeBootstrap	0.148	0.002	0.151
visVp	0.038	0.007	0.045