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This page was generated on 2022-06-24 12:07:37 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 merida1


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 942/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.16.0  (landing page)
Paul Shannon
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_15
git_last_commit: 9b7541b
git_last_commit_date: 2022-04-26 11:48:52 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: igvR
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.16.0.tar.gz
StartedAt: 2022-06-24 04:04:26 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:15:15 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 648.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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  7.2Mb
  sub-directories of 1Mb or more:
    browserCode   2.0Mb
    extdata       4.7Mb
* 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 ... 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-class0.0210.0000.024
DataFrameAnnotationTrack-class0.020.000.02
DataFrameQuantitativeTrack-class0.0120.0000.013
GFF3Track-class0.0210.0020.023
GRangesAnnotationTrack-class0.1050.0010.106
GRangesQuantitativeTrack-class0.0520.0010.055
GWASTrack-class0.0150.0010.017
GenomicAlignmentTrack-class0.2820.0040.290
UCSCBedAnnotationTrack-class0.7160.0330.751
UCSCBedGraphQuantitativeTrack-class0.2160.0190.240
VariantTrack-class1.0800.0871.173
displayTrack0.0010.0010.002
enableMotifLogoPopups0.0030.0000.003
getGenomicRegion0.0000.0000.001
getSupportedGenomes0.0000.0010.001
getTrackNames0.0010.0000.000
igvR-class0.0010.0010.002
ping0.0010.0000.001
removeTracksByName0.0040.0010.003
setCustomGenome0.0010.0000.001
setGenome000
showGenomicRegion0.0010.0010.001
trackInfo0.0020.0000.002
trackSize-DataFrameAnnotationTrack-method0.0070.0000.008
trackSize-GFF3Track-method0.0150.0010.016
trackSize-UCSCBedAnnotationTrack-method0.1990.0020.204