Multiple platform build/check report for BioC 3.6 - CHECK report for ArrayTV on veracruz1

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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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ArrayTV.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.16.0’
* 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-3.6-bioc/meat/ArrayTV.Rcheck/00check.log’
for details.


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ArrayTV")
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: BSgenome
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: rtracklayer


RUNIT TEST PROTOCOL -- Thu Apr 12 00:33:49 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ArrayTV RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  8.781   0.350  29.436

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

CHECK report for ArrayTV on veracruz1

Summary

Command output

Installation output

Tests output

Example timings