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CHECK report for BubbleTree on merida2

This page was generated on 2018-10-17 08:54:17 -0400 (Wed, 17 Oct 2018).

Package 171/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.10.0
Todd Creasy , Wei Zhu
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BubbleTree
Branch: RELEASE_3_7
Last Commit: 9cc358b
Last Changed Date: 2018-04-30 10:35:35 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2018-10-16 20:12:35 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:18:30 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 354.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

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### Running 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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BubbleTree.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.10.0’
* 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         24.482  0.097  24.756
heteroLociTrack  7.098  0.356   7.499
info             5.480  0.075   5.611
* 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-3.7-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.



Installation output

BubbleTree.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BubbleTree
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BubbleTree’ ...
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
* DONE (BubbleTree)

Tests output


Example timings

BubbleTree.Rcheck/BubbleTree-Ex.timings

nameusersystemelapsed
Annotate0.0010.0000.001
BTreePlotter0.7980.0160.820
BTreePredictor0.0100.0000.011
RBD0.0010.0000.002
RscoreTrack0.5350.0260.563
TrackPlotter0.0010.0000.001
annoByGenesAndCyto0.6010.0640.667
bafTrack0.2740.0210.295
btcompare0.0040.0060.009
btpredict3.6070.0663.706
drawBTree0.2730.0260.300
drawBubbles0.2800.0130.295
drawFeatures1.8550.0411.910
getTracks0.7050.0260.736
heteroLociTrack7.0980.3567.499
info5.4800.0755.611
loadRBD0.0340.0010.036
makeRBD24.482 0.09724.756
saveXLS0.4910.0640.575
trackBTree0.3210.0100.331
xyTrack0.3010.0150.317