Package: hiAnnotator

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiAnnotator_1.16.0.tar.gz

StartedAt: 2019-04-16 00:31:52 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:36:00 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 247.6 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 --install=check:hiAnnotator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hiAnnotator_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/hiAnnotator.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiAnnotator/DESCRIPTION’ ... OK
* this is package ‘hiAnnotator’ version ‘1.16.0’
* 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 ... 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’
get2NearestFeature: no visible binding for global variable ‘dist’
get2NearestFeature: no visible binding for global variable ‘qStrand’
get2NearestFeature: no visible binding for global variable
  ‘subjectHits’
get2NearestFeature : <anonymous>: no visible binding for global
  variable ‘queryHits’
get2NearestFeature : <anonymous>: no visible binding for global
  variable ‘dist’
get2NearestFeature : <anonymous>: no visible binding for global
  variable ‘featureName’
getFeatureCounts : <anonymous>: no visible global function definition
  for ‘countQueryHits’
getFeatureCountsBig: no visible global function definition for ‘mid’
getLowestDists: no visible binding for global variable ‘queryHits’
getLowestDists: no visible binding for global variable ‘dist’
getNearestFeature: no visible global function definition for ‘IRanges’
getNearestFeature: no visible global function definition for ‘mid’
getNearestFeature: no visible binding for global variable ‘queryHits’
getNearestFeature: no visible binding for global variable ‘n’
getNearestFeature: no visible binding for global variable ‘featureName’
getNearestFeature: no visible binding for global variable ‘dist’
getSitesInFeature: no visible global function definition for
  ‘overlapsAny’
getSitesInFeature: no visible binding for global variable ‘queryHits’
getSitesInFeature: no visible global function definition for ‘n’
getSitesInFeature: no visible binding for global variable ‘featureName’
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
  ‘seqlevelsInUse’
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 ‘seqlevelsInUse’
makeGRanges: no visible global function definition for ‘seqlengths<-’
makeGRanges: no visible global function definition for ‘seqlevels’
Undefined global functions or variables:
  IRanges breakInChunks countQueryHits detectCores dist featureName
  keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
  seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
  subjectHits
Consider adding
  importFrom("stats", "dist")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hiAnnotator
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘hiAnnotator’ ...
** R
** data
** byte-compile and prepare 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	0.001	0.000	0.002
doAnnotation	1.051	0.043	1.102
get2NearestFeature	1.989	0.098	2.107
getFeatureCounts	0.611	0.038	0.653
getFeatureCountsBig	0.600	0.029	0.640
getLowestDists	0.104	0.000	0.105
getNearestFeature	1.288	0.073	1.377
getRelevantCol	0.006	0.002	0.009
getSitesInFeature	0.730	0.035	0.775
getUCSCtable	0.001	0.000	0.000
getWindowLabel	0.000	0.000	0.001
makeChunks	0.449	0.052	0.508
makeGRanges	0.426	0.033	0.461
makeUCSCsession	0.000	0.000	0.001
plotdisFeature	1.563	0.072	1.650