BioC 3.3: CHECK report for Rariant on zin2

Package: Rariant

Version: 1.8.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rariant_1.8.3.tar.gz

StartedAt: 2016-10-13 05:44:54 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:49:31 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 276.7 seconds

RetCode: 0

Status:  OK

CheckDir: Rariant.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Rariant_1.8.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Rariant.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 ‘Rariant/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rariant’ version ‘1.8.3’
* package encoding: UTF-8
* 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 ‘Rariant’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... 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
tallyBamRegion: no visible global function definition for 'PileupParam'
tallyBamRegion: no visible global function definition for
  'ScanBamParam'
tallyBamRegion: no visible global function definition for 'pileup'
Undefined global functions or variables:
  PileupParam ScanBamParam pileup
* 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 installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘rariant-inspect-ci.png’, ‘rariant-inspect-shift.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/Rariant.Rcheck/00check.log’
for details.

* installing *source* package ‘Rariant’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (Rariant)

name	user	system	elapsed
Rariant-package	0.140	0.054	0.756
ci-adjust	0.005	0.000	0.005
ci-assessment	0.013	0.008	0.021
ci-utils	0.006	0.000	0.006
convert-utils	0.111	0.004	0.118
mismatch-plot	2.783	0.041	2.830
plot-cis	1.405	0.056	1.460
prop-cis	0.007	0.000	0.007
prop-tests	0.018	0.000	0.017
rariant	0.154	0.004	0.157
shiny	0.000	0.000	0.001
split-sample	0.001	0.003	0.001