##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:intansv.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings intansv_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/intansv.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘intansv/DESCRIPTION’ ... OK
* this is package ‘intansv’ version ‘1.42.0’
* 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 ... 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 loading without being on the library search path ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
methodsMerge   35.521  0.474  36.088
plotChromosome  6.713  0.068   6.798
plotRegion      5.442  0.771   6.556
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/intansv.Rcheck/00check.log’
for details.