Package: BubbleTree

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BubbleTree_2.14.0.tar.gz

StartedAt: 2019-10-16 01:03:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:12:01 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 504.3 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 --install=check:BubbleTree.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BubbleTree_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BubbleTree.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.14.0’
* 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 ‘BubbleTree’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 23.8Mb
  sub-directories of 1Mb or more:
    data  23.4Mb
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
makeRBD         33.723  0.244  34.105
heteroLociTrack  7.736  0.727   8.465
btpredict        6.863  0.411   7.274
info             6.980  0.174   7.214
* 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-3.9-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BubbleTree
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘BubbleTree’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BubbleTree)

name	user	system	elapsed
Annotate	0.001	0.000	0.000
BTreePlotter	0.141	0.004	0.146
BTreePredictor	0.009	0.000	0.010
RBD	0.001	0.000	0.000
RscoreTrack	0.745	0.088	0.925
TrackPlotter	0.001	0.001	0.001
annoByGenesAndCyto	0.676	0.039	0.714
bafTrack	0.244	0.032	0.277
btcompare	0.003	0.007	0.011
btpredict	6.863	0.411	7.274
drawBTree	0.341	0.065	0.406
drawBubbles	0.278	0.016	0.295
drawFeatures	2.252	0.100	2.353
getTracks	1.011	0.063	1.075
heteroLociTrack	7.736	0.727	8.465
info	6.980	0.174	7.214
loadRBD	0.030	0.002	0.034
makeRBD	33.723	0.244	34.105
saveXLS	0.614	0.142	0.795
trackBTree	0.337	0.016	0.353
xyTrack	0.309	0.028	0.338