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BioC 3.4: CHECK report for supraHex on morelia

This page was generated on 2016-09-21 03:52:36 -0700 (Wed, 21 Sep 2016).

Package 1176/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
supraHex 1.11.1
Hai Fang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/supraHex
Last Changed Rev: 118949 / Revision: 121152
Last Changed Date: 2016-06-25 09:51:00 -0700 (Sat, 25 Jun 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


supraHex.Rcheck/00install.out:

* 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)

supraHex.Rcheck/supraHex-Ex.timings:

nameusersystemelapsed
sBMH0.0560.0040.060
sCompReorder0.6170.0080.625
sDistance0.0810.0030.084
sDmat0.1550.0050.160
sDmatCluster0.2280.0080.236
sDmatMinima0.0930.0030.096
sHexDist0.0030.0000.003
sHexGrid0.0020.0000.002
sInitial0.0020.0010.002
sMapOverlay0.1510.0060.158
sNeighAny0.0050.0010.005
sNeighDirect0.0030.0000.003
sPipeline0.2870.0080.296
sTopology0.0140.0030.018
sTrainBatch0.0370.0010.039
sTrainSeq0.3470.0020.349
sTrainology0.0050.0000.005
sWriteData0.2440.0050.249
visColoralpha0.0040.0000.004
visColorbar0.0320.0010.033
visColormap0.0040.0010.004
visCompReorder1.0370.0381.077
visDmatCluster0.2830.0290.313
visDmatHeatmap0.1960.0050.202
visHeatmap0.0780.0010.079
visHeatmapAdv0.3840.0040.389
visHexAnimate0.0010.0000.001
visHexBarplot0.6580.0200.678
visHexComp0.0870.0040.092
visHexGrid0.0820.0030.085
visHexMapping0.9420.0571.000
visHexMulComp0.6380.0250.663
visHexPattern1.3930.0881.483
visKernels0.0120.0060.019
visTreeBSclust0.0710.0040.075
visTreeBootstrap0.1480.0020.151
visVp0.0380.0070.045