BioC 3.1: CHECK report for exomePeak on petty

Package: exomePeak

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings exomePeak_1.8.0.tar.gz

StartedAt: 2015-10-08 22:52:28 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:56:19 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 231.0 seconds

RetCode: 0

Status:  OK

CheckDir: exomePeak.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 exomePeak_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/exomePeak.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [24s/24s] 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:
  ‘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
  ‘makeTranscriptDb’
.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.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
  ‘makeTranscriptDbFromUCSC’
.read.gtf: no visible global function definition for
  ‘makeTranscriptDbFromGFF’
.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’
exomepeak: no visible global function definition for ‘indexBam’
* 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 ... [23s/24s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
exomepeak 10.762  0.573  11.337
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/exomePeak.Rcheck/00check.log’
for details.

* installing *source* package ‘exomePeak’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (exomePeak)

name	user	system	elapsed
bltest	0.006	0.001	0.006
ctest	0.002	0.000	0.002
exomePeak-package	0.157	0.020	0.664
exomepeak	10.762	0.573	11.337
rhtest	0.003	0.001	0.003