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This page was generated on 2024-05-21 11:37:03 -0400 (Tue, 21 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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

Package 1020/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.24.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-05-20 14:00:15 -0400 (Mon, 20 May 2024)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_19
git_last_commit: 8af20ee
git_last_commit_date: 2024-04-30 11:06:10 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for igvR on palomino3


To the developers/maintainers of the igvR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: igvR
Version: 1.24.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:igvR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings igvR_1.24.0.tar.gz
StartedAt: 2024-05-21 02:48:32 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 02:53:38 -0400 (Tue, 21 May 2024)
EllapsedTime: 306.5 seconds
RetCode: 0
Status:   OK  
CheckDir: igvR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:igvR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings igvR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/igvR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'igvR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'igvR' version '1.24.0'
* 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 whether package 'igvR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 21.8Mb
  sub-directories of 1Mb or more:
    browserCode  14.8Mb
    extdata       6.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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
.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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/igvR.Rcheck/00check.log'
for details.


Installation output

igvR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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-class0.020.000.01
DataFrameAnnotationTrack-class0.010.000.01
DataFrameQuantitativeTrack-class0.020.000.01
GFF3Track-class0.020.000.06
GRangesAnnotationTrack-class0.090.000.10
GRangesQuantitativeTrack-class0.020.000.01
GWASTrack-class0.330.031.86
GWASUrlTrack-class000
GenomicAlignmentTrack-class0.140.010.17
UCSCBedAnnotationTrack-class0.290.040.33
UCSCBedGraphQuantitativeTrack-class0.160.030.18
VariantTrack-class1.640.031.69
displayTrack000
enableMotifLogoPopups0.000.010.02
getGenomicRegion000
getSupportedGenomes000
getTrackNames000
igvR-class000
parseAndValidateGenomeSpec0.050.001.11
ping000
removeTracksByName000
setCustomGenome000
setGenome0.000.020.01
showGenomicRegion000
trackSize-DataFrameAnnotationTrack-method000
trackSize-UCSCBedAnnotationTrack-method0.090.000.10
url.exists000