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CHECK report for igvR on malbec1

This page was generated on 2021-05-06 12:27:55 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the igvR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 878/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.10.0  (landing page)
Paul Shannon
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/igvR
Branch: RELEASE_3_12
Last Commit: d74e551
Last Changed Date: 2020-10-27 11:34:57 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: igvR
Version: 1.10.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings igvR_1.10.0.tar.gz
StartedAt: 2021-05-06 02:35:12 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:42:26 -0400 (Thu, 06 May 2021)
EllapsedTime: 433.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings igvR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/igvR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.10.0’
* 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 ... 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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 ... OK
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘igvR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (igvR)

Tests output


Example timings

igvR.Rcheck/igvR-Ex.timings

nameusersystemelapsed
BedpeInteractionsTrack-class0.0200.0000.043
DataFrameAnnotationTrack-class0.0160.0000.018
DataFrameQuantitativeTrack-class0.0080.0000.011
GRangesAnnotationTrack-class0.0880.0000.092
GRangesQuantitativeTrack-class0.0400.0000.042
GenomicAlignmentTrack-class0.2680.0000.433
UCSCBedAnnotationTrack-class0.6160.0320.646
UCSCBedGraphQuantitativeTrack-class0.1520.0240.204
VariantTrack-class0.7280.0080.734
displayTrack0.0000.0000.001
enableMotifLogoPopups0.0000.0000.002
getGenomicRegion000
getSupportedGenomes0.0040.0000.000
getTrackNames000
igvR-class0.0040.0000.002
ping0.0000.0000.001
removeTracksByName0.0040.0000.003
setGenome0.0000.0000.001
showGenomicRegion0.0000.0000.001
trackInfo0.0000.0000.001
trackSize-DataFrameAnnotationTrack-method0.0080.0000.007
trackSize-UCSCBedAnnotationTrack-method0.1520.0000.150