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BioC 3.2: CHECK report for BubbleTree on oaxaca

This page was generated on 2016-04-23 10:28:54 -0700 (Sat, 23 Apr 2016).

Package 126/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.0.1
Wei Zhu
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BubbleTree
Last Changed Rev: 113112 / Revision: 116712
Last Changed Date: 2016-01-30 16:29:21 -0800 (Sat, 30 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.0.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BubbleTree_2.0.1.tar.gz
StartedAt: 2016-04-22 22:18:17 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:23:28 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 310.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BubbleTree.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BubbleTree_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/BubbleTree.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.0.1’
* 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 ... [27s/28s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘BubbleTree’
  Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘BubbleTree’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/BubbleTree.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 24.8Mb
  sub-directories of 1Mb or more:
    data  22.8Mb
    doc    1.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
It is recommended to use ‘given’ instead of ‘middle’.
* 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 ... OK
* 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 ... [38s/39s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
heteroLociTrack 6.536  0.295   6.833
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘BubbleTree’
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘BubbleTree’
Found more than one class "GenomicRanges" in cache; using the first, from namespace 'GenomicRanges'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘BubbleTree’
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘BubbleTree’
* DONE (BubbleTree)

BubbleTree.Rcheck/BubbleTree-Ex.timings:

nameusersystemelapsed
Annotate0.0010.0010.001
BTreePlotter0.0870.0010.088
BTreePredictor0.0080.0000.009
RscoreTrack0.5370.0320.571
TrackPlotter0.0010.0000.001
annoByGenesAndCyto1.0830.0341.119
bafTrack0.2770.0230.299
btcompare0.0030.0090.012
btpredict4.5970.0414.642
drawBTree0.3350.0350.370
drawBubbles0.3440.0100.355
drawFeatures1.3760.0371.482
getTracks1.1180.0291.147
heteroLociTrack6.5360.2956.833
info4.2950.0614.357
loadRBD0.0650.0020.068
saveXLS0.4120.0491.508
trackBTree0.3130.0070.320
xyTrack0.2430.0120.255