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This page was generated on 2021-11-29 15:04:57 -0500 (Mon, 29 Nov 2021).

CHECK results for hiAnnotator on nebbiolo2

To the developers/maintainers of the hiAnnotator package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/hiAnnotator.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 864/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.28.0  (landing page)
Nirav V Malani
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/hiAnnotator
git_branch: RELEASE_3_14
git_last_commit: ac0785b
git_last_commit_date: 2021-10-26 12:13:40 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: hiAnnotator
Version: 1.28.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hiAnnotator_1.28.0.tar.gz
StartedAt: 2021-11-28 09:30:49 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 09:34:21 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 212.1 seconds
RetCode: 0
Status:   OK  
CheckDir: hiAnnotator.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:hiAnnotator.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings hiAnnotator_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/hiAnnotator.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.28.0’
* 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 ‘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 ‘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’
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’
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 featureName
  keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths
  seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels
  subjectHits
* 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-3.14-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.



Installation output

hiAnnotator.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL hiAnnotator
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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
cleanColname0.0000.0000.001
doAnnotation1.8210.0331.854
get2NearestFeature1.2080.0561.264
getFeatureCounts0.5840.0280.612
getFeatureCountsBig0.6120.0070.620
getLowestDists0.0750.0010.075
getNearestFeature1.9250.0231.950
getRelevantCol0.0040.0000.005
getSitesInFeature0.6360.0000.636
getUCSCtable000
getWindowLabel000
makeChunks0.3750.0000.375
makeGRanges0.3590.0110.371
makeUCSCsession000
plotdisFeature1.0290.0191.050