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CHECK report for BubbleTree on malbec2

This page was generated on 2019-10-16 12:06:10 -0400 (Wed, 16 Oct 2019).

Package 192/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.14.0
Todd Creasy , Wei Zhu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BubbleTree
Branch: RELEASE_3_9
Last Commit: 7c64327
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.14.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BubbleTree_2.14.0.tar.gz
StartedAt: 2019-10-16 00:12:19 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:18:08 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 348.7 seconds
RetCode: 0
Status:  OK 
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BubbleTree.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BubbleTree_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BubbleTree.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.14.0’
* 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         20.493  0.003  20.549
heteroLociTrack  7.143  0.184   7.327
* 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-3.9-bioc/meat/BubbleTree.Rcheck/00check.log’
for details.



Installation output

BubbleTree.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BubbleTree
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

BubbleTree.Rcheck/BubbleTree-Ex.timings

nameusersystemelapsed
Annotate0.0010.0000.001
BTreePlotter0.0840.0000.084
BTreePredictor0.0070.0000.007
RBD000
RscoreTrack0.6320.0080.640
TrackPlotter000
annoByGenesAndCyto0.7660.0120.778
bafTrack0.3160.0000.316
btcompare0.0020.0000.002
btpredict3.7640.0873.856
drawBTree0.2600.0080.269
drawBubbles0.2290.0000.228
drawFeatures1.8550.0111.867
getTracks0.8950.0120.907
heteroLociTrack7.1430.1847.327
info4.1130.0124.125
loadRBD0.0170.0050.021
makeRBD20.493 0.00320.549
saveXLS0.4820.0930.965
trackBTree0.3590.0150.424
xyTrack0.3140.0120.356