BioC 3.0: CHECK report for CoverageView on perceval

Package: CoverageView

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CoverageView_1.2.0.tar.gz

StartedAt: 2015-04-10 00:26:27 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:32:07 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 339.9 seconds

RetCode: 0

Status:  OK

CheckDir: CoverageView.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 --no-multiarch CoverageView_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/CoverageView.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoverageView/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoverageView’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CoverageView’ can be installed ... [29s/41s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cov.interval,CoverageBamFile-CoverageBamFile: no visible global
  function definition for ‘bamFlag<-’
cov.interval,CoverageBamFile-CoverageBamFile: no visible global
  function definition for ‘scanBamFlag’
cov.interval,CoverageBamFile-CoverageBamFile: no visible global
  function definition for ‘countBam’
cov.matrix,ANY-ANY: no visible global function definition for
  ‘bamFlag<-’
cov.matrix,ANY-ANY: no visible global function definition for
  ‘scanBamFlag’
cov.matrix,ANY-ANY: no visible global function definition for
  ‘countBam’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [37s/33s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
draw.heatmap 8.447  0.299   8.906
cov.matrix   3.908  4.387   4.935
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/CoverageView.Rcheck/00check.log’
for details.

* installing *source* package ‘CoverageView’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CoverageView)

name	user	system	elapsed
CoverageBamFile-class	0.023	0.001	0.024
CoverageBigWigFile-class	0.019	0.002	0.021
cov.interval	1.745	0.047	1.804
cov.matrix	3.908	4.387	4.935
draw.heatmap	8.447	0.299	8.906
draw.profile	0.272	0.032	0.329
export.wig	0.190	0.013	0.219
genome.covplot.cumdepth	0.684	0.062	0.759
genome.covplot.depth	1.122	0.054	1.186
write.profile	0.394	0.455	0.440