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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings igvR_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/igvR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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  9.4Mb
  sub-directories of 1Mb or more:
    browserCode   5.9Mb
    extdata       2.9Mb
* 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 loading without being on the library search path ... 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
* 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 ...
  ‘v00.basicIntro.Rmd’ using ‘UTF-8’... OK
  ‘v01.stockGenome.Rmd’ using ‘UTF-8’... OK
  ‘v02.customGenome.Rmd’ using ‘UTF-8’... OK
  ‘v03.ctcfChIP.Rmd’ using ‘UTF-8’... OK
  ‘v04.pairedEnd.Rmd’ using ‘UTF-8’... OK
  ‘v05.ucscTableBrowser.Rmd’ using ‘UTF-8’... OK
  ‘v06.annotationHub.Rmd’ using ‘UTF-8’... OK
  ‘v07.gwas.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/igvR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL igvR
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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)