BubbleTree 2.2.2
Todd Creasy , Wei Zhu
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BubbleTree | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings BubbleTree_2.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/BubbleTree.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.2.2’
* 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 25.4Mb
sub-directories of 1Mb or more:
data 22.9Mb
doc 2.2Mb
* 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
annoByGenesAndCyto,Annotate : <anonymous>: no visible global function
definition for 'tail'
annoByOverlap,Annotate: no visible binding for global variable
'queryHits'
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 queryHits rainbow tail weighted.mean
Consider adding
importFrom("grDevices", "hcl", "rainbow")
importFrom("stats", "cutree", "dist", "hclust", "weighted.mean")
importFrom("utils", "tail")
to your NAMESPACE file.
* 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 20.226 0.004 20.422
heteroLociTrack 6.901 0.302 7.364
* 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-3.3-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BubbleTree)