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BioC 3.5: CHECK report for BubbleTree on oaxaca

This page was generated on 2017-03-04 16:49:08 -0500 (Sat, 04 Mar 2017).

Package 146/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.5.4
Todd Creasy , Wei Zhu , Kui Shen
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BubbleTree
Last Changed Rev: 127038 / Revision: 127142
Last Changed Date: 2017-02-28 15:25:10 -0500 (Tue, 28 Feb 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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

Command output

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


* 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.


BubbleTree.Rcheck/00install.out:

* 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)

BubbleTree.Rcheck/BubbleTree-Ex.timings:

nameusersystemelapsed
Annotate000
BTreePlotter0.1720.0040.175
BTreePredictor0.0050.0010.006
RBD000
RscoreTrack1.1990.0821.281
TrackPlotter0.0010.0010.000
annoByGenesAndCyto1.1040.0471.151
bafTrack1.0250.0271.053
btcompare0.0030.0110.014
btpredict4.7420.0184.762
drawBTree0.3580.0380.395
drawBubbles0.3360.0150.351
drawFeatures1.8260.0511.917
getTracks1.7490.0871.836
heteroLociTrack6.1160.2966.414
info5.2730.1145.392
loadRBD0.0710.0040.075
makeRBD22.342 0.07722.429
saveXLS0.3920.0690.876
trackBTree0.3110.0120.324
xyTrack0.2540.0250.278