BioC 3.5: CHECK report for ArrayTV on veracruz2

Package: ArrayTV

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayTV_1.14.0.tar.gz

StartedAt: 2017-10-18 00:34:20 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:37:31 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 190.2 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayTV.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayTV_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayTV.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayTV/DESCRIPTION’ ... OK
* this is package ‘ArrayTV’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘ArrayTV’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 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
.rescaleGC: no visible global function definition for ‘mad’
CorrectM: no visible global function definition for ‘mad’
CorrectM: no visible binding for global variable ‘mad’
CorrectM: no visible global function definition for ‘GRanges’
CorrectM: no visible global function definition for ‘IRanges’
CorrectM: no visible global function definition for ‘acf’
CorrectM: no visible binding for global variable ‘median’
calctvScore: no visible global function definition for ‘quantile’
gcFracOneRange: no visible global function definition for
  ‘letterFrequencyInSlidingView’
gcModel: no visible global function definition for ‘rowData’
gcModel: no visible global function definition for
  ‘letterFrequencyInSlidingView’
gcModelSeq: no visible global function definition for ‘genome’
gcModelSeq: no visible global function definition for ‘rowData’
gcModelSeq: no visible global function definition for
  ‘letterFrequencyInSlidingView’
priorFracs: no visible global function definition for ‘quantile’
priorFracsRestOfGenome: no visible global function definition for
  ‘letterFrequencyInSlidingView’
priorFracsRestOfGenome: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  GRanges IRanges acf genome letterFrequencyInSlidingView mad median
  quantile rowData
Consider adding
  importFrom("stats", "acf", "mad", "median", "quantile")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayTV.Rcheck/00check.log’
for details.

* installing *source* package ‘ArrayTV’ ...
** R
** inst
** preparing 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 (ArrayTV)

name	user	system	elapsed
gcCorrect-methods	0.001	0.000	0.001
gcCorrectMain	0.001	0.000	0.000
methods-computeGC	0	0	0