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This page was generated on 2022-12-06 11:06:25 -0500 (Tue, 06 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4506
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4283
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4312
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for igvR on nebbiolo2


To the developers/maintainers of the igvR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/igvR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 957/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.18.0  (landing page)
Paul Shannon
Snapshot Date: 2022-12-05 14:00:06 -0500 (Mon, 05 Dec 2022)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_16
git_last_commit: 90ee657
git_last_commit_date: 2022-11-01 11:17:43 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: igvR
Version: 1.18.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings igvR_1.18.0.tar.gz
StartedAt: 2022-12-05 21:05:19 -0500 (Mon, 05 Dec 2022)
EndedAt: 2022-12-05 21:09:35 -0500 (Mon, 05 Dec 2022)
EllapsedTime: 255.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings igvR_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/igvR.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.18.0’
* package encoding: UTF-8
* 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 ‘igvR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 16.8Mb
  sub-directories of 1Mb or more:
    browserCode  10.1Mb
    extdata       6.0Mb
* 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 ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
  v05.ucscTableBrowser.Rmd
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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
Unexported object imported by a ':::' call: ‘BrowserViz:::log’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.writeMotifLogoImagesUpdateTrackNames: no visible binding for global
  variable ‘MotifDb’
.writeMotifLogoImagesUpdateTrackNames: no visible global function
  definition for ‘seqLogo’
Undefined global functions or variables:
  MotifDb seqLogo
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
  Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored
* checking running R code from vignettes ...
  ‘v00.basicIntro.Rmd’ using ‘UTF-8’... OK
  ‘v01.stockGenome.Rmd’ using ‘UTF-8’... OK
  ‘v02.customGenome.Rmd’ using ‘UTF-8’... OK
  ‘v03.ctcfChIP.Rmd’ using ‘UTF-8’... OK
  ‘v04.pairedEnd.Rmd’ using ‘UTF-8’... OK
  ‘v05.ucscTableBrowser.Rmd’ using ‘UTF-8’... OK
  ‘v06.annotationHub.Rmd’ using ‘UTF-8’... OK
  ‘v07.gwas.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘igvR’ ...
** using staged installation
** R
** inst
** 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 (igvR)

Tests output


Example timings

igvR.Rcheck/igvR-Ex.timings

nameusersystemelapsed
BedpeInteractionsTrack-class0.0160.0040.020
DataFrameAnnotationTrack-class0.010.000.01
DataFrameQuantitativeTrack-class0.0150.0030.019
GFF3Track-class0.0180.0010.018
GRangesAnnotationTrack-class0.9710.0431.016
GRangesQuantitativeTrack-class0.0180.0010.018
GWASTrack-class0.1100.0000.109
GWASUrlTrack-class0.0030.0000.002
GenomicAlignmentTrack-class0.1220.0030.126
UCSCBedAnnotationTrack-class0.2980.0600.357
UCSCBedGraphQuantitativeTrack-class0.0870.0130.098
VariantTrack-class0.4270.0560.484
displayTrack0.0000.0000.001
enableMotifLogoPopups0.0000.0000.001
getGenomicRegion0.0000.0000.001
getSupportedGenomes000
getTrackNames0.0000.0000.001
igvR-class0.0010.0000.001
parseAndValidateGenomeSpec0.0890.0081.351
ping0.0010.0000.000
removeTracksByName0.0020.0000.002
setCustomGenome0.0010.0000.001
setGenome000
showGenomicRegion000
trackSize-DataFrameAnnotationTrack-method0.0030.0020.005
trackSize-UCSCBedAnnotationTrack-method0.0940.0230.118
url.exists000