BioC 3.0: CHECK report for GenomicFiles on oaxaca

Package: GenomicFiles

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GenomicFiles_1.2.1.tar.gz

StartedAt: 2015-04-09 23:54:07 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:58:44 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 276.7 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicFiles.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 GenomicFiles_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GenomicFiles.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicFiles/DESCRIPTION’ ... OK
* this is package ‘GenomicFiles’ version ‘1.2.1’
* 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 ‘GenomicFiles’ can be installed ... [22s/22s] 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.summarizeView: no visible global function definition for ‘DataFrame’
BamFileViews: no visible global function definition for ‘DataFrame’
BigWigFileViews: no visible global function definition for ‘DataFrame’
FaFileViews: no visible global function definition for ‘DataFrame’
BamFileViews,BamFileList: no visible global function definition for
  ‘DataFrame’
BamFileViews,character: no visible global function definition for
  ‘DataFrame’
BamFileViews,missing: no visible global function definition for
  ‘DataFrame’
BigWigFileViews,BigWigFileList: no visible global function definition
  for ‘DataFrame’
BigWigFileViews,character: no visible global function definition for
  ‘DataFrame’
BigWigFileViews,missing: no visible global function definition for
  ‘DataFrame’
FaFileViews,FaFileList: no visible global function definition for
  ‘DataFrame’
FaFileViews,character: no visible global function definition for
  ‘DataFrame’
FaFileViews,missing: no visible global function definition for
  ‘DataFrame’
GenomicFiles,missing-missing: no visible global function definition for
  ‘DataFrame’
exptData<-,GenomicFiles-list: no visible global function definition for
  ‘SimpleList’
unpack,list-GRangesList: no visible global function definition for
  ‘List’
* 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 ... [42s/66s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
reduceBy-methods      24.357  0.817  26.571
BigWigFileViews-class  5.312  0.016   5.491
reduceByYield          0.286  0.069  22.947
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘GenomicFiles_unit_tests.R’ [10s/10s]
 [11s/11s] 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

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

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

name	user	system	elapsed
BamFileViews-class	0.216	0.009	0.226
BigWigFileViews-class	5.312	0.016	5.491
FaFileViews-class	0.037	0.002	0.054
GenomicFileViews-class	0.022	0.001	0.022
GenomicFiles-class	0.066	0.001	0.067
pack-methods	0.886	0.002	0.896
reduceBy-methods	24.357	0.817	26.571
reduceByYield	0.286	0.069	22.947
registry-utils	0.001	0.000	0.002
unpack-methods	0.978	0.015	0.994