BioC 3.5: CHECK report for Rariant on veracruz2

Package: Rariant

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rariant_1.12.0.tar.gz

StartedAt: 2017-08-16 07:05:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:12:39 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 410.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rariant.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rariant_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rariant.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.0’
* 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  8.9Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    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 ... WARNING
Found the following significant warnings:

  Warning: 'rbind_all' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
               user system elapsed
mismatch-plot 7.738  0.143   7.984
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rariant.Rcheck/00check.log’
for details.

* installing *source* package ‘Rariant’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (Rariant)

name	user	system	elapsed
Rariant-package	0.151	0.028	0.199
ci-adjust	0.004	0.000	0.005
ci-assessment	0.018	0.000	0.018
ci-utils	0.006	0.001	0.006
convert-utils	0.951	0.004	0.978
mismatch-plot	7.738	0.143	7.984
plot-cis	1.220	0.007	1.245
prop-cis	0.007	0.000	0.007
prop-tests	0.013	0.001	0.014
rariant	0.145	0.004	0.151
shiny	0.001	0.000	0.000
split-sample	0.002	0.000	0.002