BubbleTree 2.3.4
Todd Creasy , Wei Zhu
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BubbleTree | | Last Changed Rev: 118811 / Revision: 121152 | | Last Changed Date: 2016-06-21 08:54:27 -0700 (Tue, 21 Jun 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BubbleTree_2.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BubbleTree.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.3.4’
* 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 ... 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 20.798 0.084 20.899
heteroLociTrack 6.017 0.263 6.282
* 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.
* 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)