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This page was generated on 2023-02-04 11:04:56 -0500 (Sat, 04 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 nebbiolo1


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 946/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.19.0  (landing page)
Paul Shannon
Snapshot Date: 2023-02-03 14:00:22 -0500 (Fri, 03 Feb 2023)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: master
git_last_commit: 631282a
git_last_commit_date: 2022-11-01 11:17:43 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    NA  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: igvR
Version: 1.19.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings igvR_1.19.0.tar.gz
StartedAt: 2023-02-03 21:22:46 -0500 (Fri, 03 Feb 2023)
EndedAt: 2023-02-03 21:27:25 -0500 (Fri, 03 Feb 2023)
EllapsedTime: 279.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings igvR_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/igvR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.19.0’
* 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  7.3Mb
  sub-directories of 1Mb or more:
    browserCode   4.1Mb
    extdata       2.6Mb
* 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-3.17-bioc/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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-class0.0090.0030.013
DataFrameAnnotationTrack-class0.0070.0050.013
DataFrameQuantitativeTrack-class0.0190.0040.023
GFF3Track-class0.0130.0000.014
GRangesAnnotationTrack-class0.0650.0110.077
GRangesQuantitativeTrack-class0.0210.0040.025
GWASTrack-class0.1430.0170.161
GWASUrlTrack-class0.0010.0030.003
GenomicAlignmentTrack-class0.1630.0020.167
UCSCBedAnnotationTrack-class0.3440.0080.352
UCSCBedGraphQuantitativeTrack-class0.1030.0070.111
VariantTrack-class0.5870.0320.620
displayTrack0.0010.0000.001
enableMotifLogoPopups0.0000.0000.001
getGenomicRegion0.0000.0000.001
getSupportedGenomes000
getTrackNames000
igvR-class0.0010.0000.000
parseAndValidateGenomeSpec0.2830.0041.436
ping0.0000.0000.001
removeTracksByName0.0030.0000.003
setCustomGenome0.0020.0000.001
setGenome0.0000.0000.001
showGenomicRegion0.0000.0010.001
trackSize-DataFrameAnnotationTrack-method0.0080.0000.008
trackSize-UCSCBedAnnotationTrack-method0.1230.0000.124
url.exists000