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This page was generated on 2023-10-20 09:38:04 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 981/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.20.0  (landing page)
Paul Shannon
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: RELEASE_3_17
git_last_commit: 274e1a2
git_last_commit_date: 2023-04-25 11:01:27 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for igvR on kjohnson2


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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2023-10-18 01:37:28 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 01:46:11 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 522.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: igvR.Rcheck
Warnings: 3

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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/igvR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.20.0’
* 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 ... 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 startup messages can be suppressed ... 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
.displayQuantitativeTrack: no visible global function definition for
  ‘printf’
.writeMotifLogoImagesUpdateTrackNames: no visible binding for global
  variable ‘MotifDb’
.writeMotifLogoImagesUpdateTrackNames: no visible global function
  definition for ‘seqLogo’
Undefined global functions or variables:
  MotifDb printf 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 ... WARNING
Documented arguments not in \usage in documentation object 'GWASUrlTrack':
  ‘color’

Undocumented arguments in documentation object 'QuantitativeTrack-class'
  ‘trackHeight’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
parseAndValidateGenomeSpec 0.113  0.046   7.365
* 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: 3 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

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###
### 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-class0.0140.0020.028
DataFrameAnnotationTrack-class0.0130.0010.020
DataFrameQuantitativeTrack-class0.0220.0020.036
GFF3Track-class0.0160.0020.028
GRangesAnnotationTrack-class0.0790.0030.125
GRangesQuantitativeTrack-class0.0190.0010.029
GWASTrack-class0.1480.0090.246
GWASUrlTrack-class0.0050.0010.007
GenomicAlignmentTrack-class0.1860.0160.303
UCSCBedAnnotationTrack-class0.5050.0100.786
UCSCBedGraphQuantitativeTrack-class0.1200.0050.189
VariantTrack-class1.4500.0512.303
displayTrack0.0010.0000.001
enableMotifLogoPopups0.0010.0000.001
getGenomicRegion0.0000.0000.002
getSupportedGenomes0.0000.0010.001
getTrackNames000
igvR-class0.0010.0000.002
parseAndValidateGenomeSpec0.1130.0467.365
ping000
removeTracksByName0.0020.0010.006
setCustomGenome0.0000.0010.001
setGenome0.0000.0010.000
showGenomicRegion0.0000.0000.001
trackSize-DataFrameAnnotationTrack-method0.0050.0000.008
trackSize-UCSCBedAnnotationTrack-method0.1210.0030.200
url.exists000