BioC 3.4: CHECK report for BubbleTree on zin1

Package: BubbleTree

Version: 2.3.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BubbleTree_2.3.4.tar.gz

StartedAt: 2016-09-20 03:56:28 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:00:43 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 255.6 seconds

RetCode: 0

Status:  OK

CheckDir: BubbleTree.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BubbleTree_2.3.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BubbleTree.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BubbleTree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BubbleTree’ version ‘2.3.4’
* 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 ‘BubbleTree’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 25.4Mb
  sub-directories of 1Mb or more:
    data  22.9Mb
    doc    2.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Annotate: no visible global function definition for 'new'
BTreePlotter: no visible global function definition for 'new'
BTreePredictor: no visible global function definition for 'new'
RBD: no visible global function definition for 'new'
TrackPlotter: no visible global function definition for 'new'
gr: no visible global function definition for 'new'
gr2: no visible global function definition for 'new'
annoByGenesAndCyto,Annotate : <anonymous>: no visible global function
  definition for 'tail'
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
btpredict,BTreePredictor: no visible global function definition for
  'new'
btpredict,BTreePredictor : <anonymous>: no visible binding for global
  variable 'dist'
btpredict,BTreePredictor: no visible binding for global variable 'dist'
findBestXYP,BTreePredictor: no visible binding for global variable
  'dist'
findClones,BTreePredictor : <anonymous>: no visible binding for global
  variable 'dist'
findClones,BTreePredictor: no visible global function definition for
  'cutree'
findClones,BTreePredictor: no visible global function definition for
  'hclust'
findClones,BTreePredictor: no visible global function definition for
  'dist'
findClones,BTreePredictor: no visible global function definition for
  'weighted.mean'
getPloidyAdj,BTreePredictor: no visible global function definition for
  'weighted.mean'
initialize,BTreePlotter : gg_color_hue: no visible global function
  definition for 'hcl'
initialize,BTreePlotter: no visible global function definition for
  'rainbow'
Undefined global functions or variables:
  cutree dist hcl hclust new queryHits rainbow tail weighted.mean
Consider adding
  importFrom("grDevices", "hcl", "rainbow")
  importFrom("methods", "new")
  importFrom("stats", "cutree", "dist", "hclust", "weighted.mean")
  importFrom("utils", "tail")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
makeRBD         19.392  0.008  19.405
heteroLociTrack  6.344  0.976   7.324
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.

* installing *source* package ‘BubbleTree’ ...
It is recommended to use ‘given’ instead of ‘middle’.
** 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 (BubbleTree)

name	user	system	elapsed
Annotate	0	0	0
BTreePlotter	0.076	0.000	0.079
BTreePredictor	0.004	0.000	0.006
RBD	0.004	0.000	0.001
RscoreTrack	0.340	0.016	0.357
TrackPlotter	0	0	0
annoByGenesAndCyto	0.456	0.016	0.472
bafTrack	0.608	0.020	0.627
btcompare	0.004	0.000	0.003
btpredict	3.696	0.028	3.725
drawBTree	0.252	0.088	0.340
drawBubbles	0.264	0.024	0.289
drawFeatures	1.004	0.068	1.071
getTracks	0.956	0.012	0.969
heteroLociTrack	6.344	0.976	7.324
info	4.004	0.008	4.016
loadRBD	0.072	0.004	0.076
makeRBD	19.392	0.008	19.405
saveXLS	0.336	0.048	0.531
trackBTree	0.272	0.020	0.291
xyTrack	0.216	0.016	0.233