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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CNVRanger_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CNVRanger.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* this is package ‘CNVRanger’ version ‘1.23.0’
* 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 ‘CNVRanger’ 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'rappdirs:::get_os'
  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
plotRecurrentRegions: no visible binding for global variable ‘type’
plotRecurrentRegions: no visible binding for global variable ‘pvalue’
Undefined global functions or variables:
  pvalue type
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cnvEQTL.Rd: GRanges-class, GRangesList-class, RaggedExperiment-class,
    RangedSummarizedExperiment-class, qreduceAssay, filterByExpr,
    DataFrame-class, findOverlaps, glmQLFit, glmQLFTest
  cnvOncoPrint.Rd: GRangesList-class, RaggedExperiment-class,
    GRanges-class, qreduceAssay
  plotEQTL.Rd: GRanges-class
  plotManhattan.Rd: GRanges-class
  plotRecurrentRegions.Rd: GRanges-class
  populationRanges.Rd: GRangesList-class, GRanges-class, findOverlaps
  setupCnvGWAS.Rd: RaggedExperiment-class, GRangesList-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
plotEQTL             19.136  1.453  31.929
plotRecurrentRegions 14.873  0.615  18.481
plotManhattan         6.313  0.471   6.785
cnvGWAS               5.276  0.093   5.369
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CNVRanger.Rcheck/00check.log’
for details.