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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:intansv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings intansv_1.44.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.44.0’
* 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 ‘intansv’ can be installed ... OK
* checking installed package size ... OK
* 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 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
DellyCluster: no visible global function definition for 'subjectHits'
LumpyCluster: no visible global function definition for 'subjectHits'
PindelCluster: no visible global function definition for 'subjectHits'
breakDancerCluster: no visible global function definition for
  'subjectHits'
mergeOLCNVs: no visible global function definition for 'subjectHits'
methodsMerge: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for 'queryHits'
plotChromosome: no visible global function definition for 'subjectHits'
plotChromosome: no visible global function definition for
  'seqlengths<-'
plotChromosome: no visible global function definition for 'seqlengths'
plotChromosome: no visible global function definition for 'aes'
plotRegion: no visible global function definition for 'seqlengths<-'
plotRegion: no visible global function definition for 'subjectHits'
plotRegion: no visible global function definition for 'aes'
plotRegion: no visible binding for global variable 'name'
readCnvnator: no visible global function definition for 'subjectHits'
readDelly: no visible global function definition for 'subjectHits'
readLumpy: no visible global function definition for 'subjectHits'
readPindel: no visible global function definition for 'subjectHits'
readSoftSearch: no visible global function definition for 'subjectHits'
readSvseq: no visible global function definition for 'subjectHits'
readSvseq : <anonymous>: no visible global function definition for
  'subjectHits'
softSearchCluster: no visible global function definition for
  'subjectHits'
tellOLPercantage: no visible global function definition for 'queryHits'
tellOLPercantage: no visible global function definition for
  'subjectHits'
Undefined global functions or variables:
  aes name queryHits seqlengths seqlengths<- subjectHits
* checking Rd files ... NOTE
checkRd: (-1) plotChromosome.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotChromosome.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotChromosome.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotChromosome.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotChromosome.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotRegion.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotRegion.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotRegion.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plotRegion.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) svAnnotation.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) svAnnotation.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) svAnnotation.Rd:32: Lost braces in \itemize; meant \describe ?
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
methodsMerge   23.384  0.351  35.164
plotRegion      6.475  0.065   9.684
plotChromosome  5.651  0.082   8.357
readLumpy       3.979  0.037   6.048
readDelly       3.542  0.033   5.405
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/intansv.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL intansv
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘intansv’ ...
** 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 (intansv)