BioC 3.5: CHECK report for exomePeak on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings exomePeak_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/exomePeak.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 ‘exomePeak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘exomePeak’ version ‘2.10.0’
* 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 ‘exomePeak’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘GenomicAlignments’ ‘GenomicFeatures’ ‘Rsamtools’ ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bed2grangeslist: no visible global function definition for ‘head’
.bed2grangeslist: no visible global function definition for ‘makeTxDb’
.bed2grangeslist: no visible global function definition for ‘exonsBy’
.exomepeak_notification: no visible global function definition for
  ‘mcols<-’
.get.bam.chrs: no visible global function definition for ‘indexBam’
.get.bam.chrs: no visible global function definition for ‘ScanBamParam’
.get.bam.chrs: no visible global function definition for ‘scanBam’
.get.bam.read.length: no visible global function definition for
  ‘indexBam’
.get.bam.read.length: no visible global function definition for
  ‘ScanBamParam’
.get.bam.read.length: no visible global function definition for
  ‘scanBam’
.get.bam.read.length: no visible global function definition for
  ‘median’
.get.check.points.reads.count: no visible global function definition
  for ‘RangesList’
.get.check.points.reads.count: no visible global function definition
  for ‘IRanges’
.get.check.points.reads.count: no visible global function definition
  for ‘ScanBamParam’
.get.check.points.reads.count: no visible global function definition
  for ‘scanBam’
.read.gtf: no visible global function definition for ‘makeTxDbFromUCSC’
.read.gtf: no visible global function definition for ‘makeTxDbFromGFF’
.read.gtf: no visible global function definition for ‘keys’
.read.gtf: no visible global function definition for ‘select’
.read.gtf: no visible global function definition for ‘columns’
.readTxDb2: no visible global function definition for
  ‘makeTxDbFromUCSC’
.readTxDb2: no visible global function definition for ‘makeTxDbFromGFF’
.report.diff.peak.based.on.result: no visible global function
  definition for ‘write.table’
.report.peak.based.on.result: no visible global function definition for
  ‘write.table’
.xls2Grangeslist: no visible global function definition for
  ‘read.table’
.xls2Grangeslist: no visible global function definition for ‘head’
.xls2Grangeslist: no visible global function definition for ‘makeTxDb’
.xls2Grangeslist: no visible global function definition for ‘exonsBy’
.xls2Grangeslist: no visible global function definition for ‘mcols<-’
RMT: no visible global function definition for ‘read.table’
RMT: no visible global function definition for ‘write.table’
RMT: no visible global function definition for ‘findOverlaps’
RMT: no visible global function definition for ‘queryHits’
RMT: no visible global function definition for ‘subjectHits’
RMT: no visible global function definition for ‘ranges’
RMT: no visible global function definition for ‘exonsBy’
RMT: no visible global function definition for ‘readGAlignments’
RMT: no visible global function definition for ‘ScanBamParam’
RMT: no visible global function definition for ‘scanBam’
RMT: no visible global function definition for ‘countOverlaps’
RMT: no visible global function definition for ‘width’
RMT: no visible global function definition for ‘var’
bltest: no visible global function definition for ‘pchisq’
bltest: no visible global function definition for ‘p.adjust’
ctest: no visible global function definition for ‘pbinom’
ctest: no visible global function definition for ‘p.adjust’
exomepeak: no visible global function definition for ‘indexBam’
rhtest: no visible global function definition for ‘phyper’
rhtest: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  IRanges RangesList ScanBamParam columns countOverlaps exonsBy
  findOverlaps head indexBam keys makeTxDb makeTxDbFromGFF
  makeTxDbFromUCSC mcols<- median p.adjust pbinom pchisq phyper
  queryHits ranges read.table readGAlignments scanBam select
  subjectHits var width write.table
Consider adding
  importFrom("stats", "median", "p.adjust", "pbinom", "pchisq", "phyper",
             "var")
  importFrom("utils", "head", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: RMT.Rd:60-62: Dropping empty section \details
prepare_Rd: RMT.Rd:74-76: Dropping empty section \note
prepare_Rd: RMT.Rd:80-82: Dropping empty section \seealso
* 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
Examples with CPU or elapsed time > 5s
            user system elapsed
RMT       20.974  0.417  21.942
exomepeak  5.644  0.193   5.954
* 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/exomePeak.Rcheck/00check.log’
for details.
BioC 3.5: CHECK report for exomePeak on veracruz2

Summary

Command output

name	user	system	elapsed
RMT	20.974	0.417	21.942
bltest	0.002	0.000	0.002
ctest	0.001	0.000	0.001
exomePeak-package	0.094	0.012	0.113
exomepeak	5.644	0.193	5.954
rhtest	0.002	0.000	0.003