BioC 3.2: CHECK report for BubbleTree on zin1

Package: BubbleTree

Version: 2.0.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BubbleTree_2.0.1.tar.gz

StartedAt: 2016-04-22 22:39:49 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:44:01 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 252.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BubbleTree.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BubbleTree_2.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BubbleTree.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘2.0.1’
* 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 ... [22s/22s] WARNING
Found the following significant warnings:
  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 ‘/home/biocbuild/bbs-3.2-bioc/meat/BubbleTree.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 24.5Mb
  sub-directories of 1Mb or more:
    data  22.8Mb
    doc    1.5Mb
* 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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
heteroLociTrack 6.212  0.076   6.283
* 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
  ‘/home/biocbuild/bbs-3.2-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: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘BubbleTree’
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: replacing previous import ‘BiocGenerics::combine’ by ‘gridExtra::combine’ when loading ‘BubbleTree’
* DONE (BubbleTree)

name	user	system	elapsed
Annotate	0.001	0.000	0.000
BTreePlotter	0.074	0.000	0.074
BTreePredictor	0.007	0.000	0.008
RscoreTrack	0.384	0.008	0.391
TrackPlotter	0.000	0.000	0.001
annoByGenesAndCyto	0.903	0.032	0.934
bafTrack	0.219	0.004	0.223
btcompare	0.003	0.000	0.003
btpredict	3.485	0.028	3.511
drawBTree	0.259	0.004	0.263
drawBubbles	0.274	0.000	0.273
drawFeatures	1.025	0.004	1.029
getTracks	0.983	0.000	0.982
heteroLociTrack	6.212	0.076	6.283
info	3.760	0.008	3.769
loadRBD	0.075	0.000	0.075
saveXLS	0.321	0.021	0.360
trackBTree	0.276	0.012	0.288
xyTrack	0.232	0.000	0.233