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This page was generated on 2024-03-28 11:32:22 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 1006/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.22.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_18
git_last_commit: ace7a89
git_last_commit_date: 2023-10-24 11:04:57 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for igvR on kjohnson1


To the developers/maintainers of the igvR package:
- 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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2024-03-27 16:24:17 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 16:30:09 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 351.8 seconds
RetCode: 0
Status:   OK  
CheckDir: igvR.Rcheck
Warnings: 0

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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/igvR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.22.0’
* 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 21.8Mb
  sub-directories of 1Mb or more:
    browserCode  14.9Mb
    extdata       6.3Mb
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/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-class0.0110.0010.014
DataFrameAnnotationTrack-class0.0120.0010.012
DataFrameQuantitativeTrack-class0.0230.0010.024
GFF3Track-class0.0160.0020.018
GRangesAnnotationTrack-class0.0690.0020.072
GRangesQuantitativeTrack-class0.0160.0000.017
GWASTrack-class0.1480.0050.155
GWASUrlTrack-class0.0040.0000.004
GenomicAlignmentTrack-class0.1610.0100.173
UCSCBedAnnotationTrack-class1.4990.0141.516
UCSCBedGraphQuantitativeTrack-class0.0950.0030.100
VariantTrack-class0.5270.0360.564
displayTrack0.0010.0000.001
enableMotifLogoPopups0.0010.0010.002
getGenomicRegion000
getSupportedGenomes0.0000.0010.000
getTrackNames000
igvR-class0.0010.0010.001
parseAndValidateGenomeSpec0.0940.0151.249
ping0.0000.0000.001
removeTracksByName0.0030.0000.003
setCustomGenome0.0010.0010.001
setGenome000
showGenomicRegion0.0000.0010.000
trackSize-DataFrameAnnotationTrack-method0.0040.0000.005
trackSize-UCSCBedAnnotationTrack-method0.1010.0100.111
url.exists0.0000.0010.001