BioC 3.5: CHECK report for BubbleTree on oaxaca

Package: BubbleTree

Version: 2.5.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BubbleTree_2.5.4.tar.gz

StartedAt: 2017-03-03 23:52:32 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:58:08 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 335.7 seconds

RetCode: 0

Status:  OK

CheckDir: BubbleTree.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 BubbleTree_2.5.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BubbleTree.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 ‘BubbleTree/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BubbleTree’ version ‘2.5.4’
* 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 25.9Mb
  sub-directories of 1Mb or more:
    data  22.9Mb
    doc    2.7Mb
* 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
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
Undefined global functions or variables:
  queryHits
* 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         22.342  0.077  22.429
heteroLociTrack  6.116  0.296   6.414
info             5.273  0.114   5.392
* 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/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	0.172	0.004	0.175
BTreePredictor	0.005	0.001	0.006
RBD	0	0	0
RscoreTrack	1.199	0.082	1.281
TrackPlotter	0.001	0.001	0.000
annoByGenesAndCyto	1.104	0.047	1.151
bafTrack	1.025	0.027	1.053
btcompare	0.003	0.011	0.014
btpredict	4.742	0.018	4.762
drawBTree	0.358	0.038	0.395
drawBubbles	0.336	0.015	0.351
drawFeatures	1.826	0.051	1.917
getTracks	1.749	0.087	1.836
heteroLociTrack	6.116	0.296	6.414
info	5.273	0.114	5.392
loadRBD	0.071	0.004	0.075
makeRBD	22.342	0.077	22.429
saveXLS	0.392	0.069	0.876
trackBTree	0.311	0.012	0.324
xyTrack	0.254	0.025	0.278