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CHECK report for hiAnnotator on malbec1

This page was generated on 2020-11-23 12:13:00 -0500 (Mon, 23 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE hiAnnotator PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 827/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.24.0
Nirav V Malani
Snapshot Date: 2020-11-22 14:42:09 -0500 (Sun, 22 Nov 2020)
URL: https://git.bioconductor.org/packages/hiAnnotator
Branch: RELEASE_3_12
Last Commit: ab43fdd
Last Changed Date: 2020-10-27 10:56:46 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hiAnnotator
Version: 1.24.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hiAnnotator_1.24.0.tar.gz
StartedAt: 2020-11-23 03:01:33 -0500 (Mon, 23 Nov 2020)
EndedAt: 2020-11-23 03:06:23 -0500 (Mon, 23 Nov 2020)
EllapsedTime: 290.7 seconds
RetCode: 0
Status:  OK 
CheckDir: hiAnnotator.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hiAnnotator_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/hiAnnotator.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiAnnotator/DESCRIPTION’ ... OK
* this is package ‘hiAnnotator’ version ‘1.24.0’
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.



Installation output

hiAnnotator.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL hiAnnotator
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘hiAnnotator’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hiAnnotator)

Tests output


Example timings

hiAnnotator.Rcheck/hiAnnotator-Ex.timings

nameusersystemelapsed
cleanColname0.0040.0000.002
doAnnotation2.5400.0402.588
get2NearestFeature1.6160.0641.687
getFeatureCounts0.7040.0200.723
getFeatureCountsBig0.6120.0000.613
getLowestDists0.0800.0000.082
getNearestFeature1.3760.0081.382
getRelevantCol0.0040.0040.009
getSitesInFeature0.6880.0120.704
getUCSCtable0.0000.0000.001
getWindowLabel000
makeChunks0.4240.0080.432
makeGRanges0.3920.0040.393
makeUCSCsession000
plotdisFeature2.7800.0122.800