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BioC 3.4: CHECK report for BubbleTree on morelia

This page was generated on 2017-04-15 16:26:16 -0400 (Sat, 15 Apr 2017).

Package 147/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.4.0
Todd Creasy , Wei Zhu
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/BubbleTree
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BubbleTree_2.4.0.tar.gz
StartedAt: 2017-04-14 23:24:24 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:29:30 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 305.8 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BubbleTree.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.4.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/BubbleTree.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 25.8Mb
  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
Annotate: no visible global function definition for 'new'
BTreePlotter: no visible global function definition for 'new'
BTreePredictor: no visible global function definition for 'new'
RBD: no visible global function definition for 'new'
TrackPlotter: no visible global function definition for 'new'
gr: no visible global function definition for 'new'
gr2: no visible global function definition for 'new'
annoByGenesAndCyto,Annotate : <anonymous>: no visible global function
  definition for 'tail'
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
btpredict,BTreePredictor: no visible global function definition for
  'new'
btpredict,BTreePredictor : <anonymous>: no visible binding for global
  variable 'dist'
btpredict,BTreePredictor: no visible binding for global variable 'dist'
findBestXYP,BTreePredictor: no visible binding for global variable
  'dist'
findClones,BTreePredictor : <anonymous>: no visible binding for global
  variable 'dist'
findClones,BTreePredictor: no visible global function definition for
  'cutree'
findClones,BTreePredictor: no visible global function definition for
  'hclust'
findClones,BTreePredictor: no visible global function definition for
  'dist'
findClones,BTreePredictor: no visible global function definition for
  'weighted.mean'
getPloidyAdj,BTreePredictor: no visible global function definition for
  'weighted.mean'
initialize,BTreePlotter : gg_color_hue: no visible global function
  definition for 'hcl'
initialize,BTreePlotter: no visible global function definition for
  'rainbow'
Undefined global functions or variables:
  cutree dist hcl hclust new queryHits rainbow tail weighted.mean
Consider adding
  importFrom("grDevices", "hcl", "rainbow")
  importFrom("methods", "new")
  importFrom("stats", "cutree", "dist", "hclust", "weighted.mean")
  importFrom("utils", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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         19.046  0.049  19.219
heteroLociTrack  5.430  0.235   5.666
* 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-3.4-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 in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (BubbleTree)

BubbleTree.Rcheck/BubbleTree-Ex.timings:

nameusersystemelapsed
Annotate0.0010.0000.057
BTreePlotter0.0850.0010.085
BTreePredictor0.0050.0000.006
RBD0.0010.0000.001
RscoreTrack0.3860.0300.415
TrackPlotter0.0010.0000.000
annoByGenesAndCyto0.4240.0290.453
bafTrack0.6780.0270.706
btcompare0.0030.0080.010
btpredict3.1610.0344.519
drawBTree0.2380.0290.267
drawBubbles0.2700.0110.280
drawFeatures1.3280.0401.448
getTracks0.5020.0290.531
heteroLociTrack5.4300.2355.666
info3.5440.0503.595
loadRBD0.0680.0050.074
makeRBD19.046 0.04919.219
saveXLS0.3630.0570.921
trackBTree0.2810.0100.291
xyTrack0.2460.0220.269