BioC 3.0: CHECK report for hiAnnotator on perceval

Package: hiAnnotator

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch hiAnnotator_1.0.0.tar.gz

StartedAt: 2015-04-10 02:41:14 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:47:15 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 361.2 seconds

RetCode: 0

Status:  OK

CheckDir: hiAnnotator.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 hiAnnotator_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/hiAnnotator.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 ‘hiAnnotator/DESCRIPTION’ ... OK
* this is package ‘hiAnnotator’ version ‘1.0.0’
* 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 ‘hiAnnotator’ can be installed ... [31s/32s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get2NearestFeature: no visible global function definition for ‘IRanges’
get2NearestFeature: no visible global function definition for ‘mid’
getFeatureCounts : <anonymous>: no visible global function definition
  for ‘countQueryHits’
getFeatureCountsBig: no visible global function definition for ‘mid’
getNearestFeature: no visible global function definition for ‘IRanges’
getNearestFeature: no visible global function definition for ‘mid’
makeChunks: no visible global function definition for ‘breakInChunks’
makeChunks: no visible global function definition for ‘detectCores’
makeChunks : <anonymous>: no visible global function definition for
  ‘keepSeqlevels’
makeChunks : <anonymous>: no visible global function definition for
  ‘seqlevels’
makeGRanges: no visible global function definition for ‘IRanges’
makeGRanges: no visible global function definition for ‘seqlengths’
makeGRanges: no visible global function definition for ‘seqlevels<-’
makeGRanges: no visible global function definition for ‘sortSeqlevels’
makeGRanges: no visible global function definition for ‘seqlevels’
makeGRanges: no visible global function definition for ‘seqlengths<-’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
get2NearestFeature 9.714  0.124    9.86
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [18s/18s]
 [18s/18s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.

* installing *source* package ‘hiAnnotator’ ...
** 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 (hiAnnotator)

name	user	system	elapsed
cleanColname	0.002	0.000	0.002
doAnnotation	3.869	0.125	4.000
get2NearestFeature	9.714	0.124	9.860
getFeatureCounts	4.412	0.064	4.479
getFeatureCountsBig	4.218	0.069	4.287
getLowestDists	0.149	0.001	0.150
getNearestFeature	3.859	0.119	3.997
getRelevantCol	0.008	0.004	0.011
getSitesInFeature	2.209	0.043	2.263
getUCSCtable	0.001	0.000	0.000
getWindowLabel	0.001	0.001	0.001
makeChunks	1.225	0.055	1.281
makeGRanges	0.619	0.054	0.673
makeUCSCsession	0.001	0.000	0.001
plotdisFeature	2.959	0.073	3.044