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CHECK report for BubbleTree on malbec2

This page was generated on 2019-04-09 11:41:19 -0400 (Tue, 09 Apr 2019).

Package 189/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.13.3
Todd Creasy , Wei Zhu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/BubbleTree
Branch: master
Last Commit: 90efc88
Last Changed Date: 2019-01-04 10:51:02 -0400 (Fri, 04 Jan 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: BubbleTree
Version: 2.13.3
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_2.13.3.tar.gz
StartedAt: 2019-04-08 23:08:21 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:13:59 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 337.7 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_2.13.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BubbleTree.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.13.3’
* 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         18.329  0.020  18.388
heteroLociTrack  6.500  0.176   6.685
* 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
Annotate000
BTreePlotter0.0860.0000.086
BTreePredictor0.0070.0000.007
RBD000
RscoreTrack0.6390.0080.647
TrackPlotter0.0010.0000.001
annoByGenesAndCyto0.7680.0040.772
bafTrack0.3010.0120.313
btcompare0.0030.0000.004
btpredict2.4090.0322.441
drawBTree0.2410.0080.249
drawBubbles0.2320.0080.240
drawFeatures1.1220.0001.122
getTracks1.2300.0001.231
heteroLociTrack6.5000.1766.685
info3.8370.0123.850
loadRBD0.0250.0000.025
makeRBD18.329 0.02018.388
saveXLS0.4600.1021.030
trackBTree0.4230.0160.441
xyTrack0.3000.0110.317