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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CNVRanger.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CNVRanger_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CNVRanger/DESCRIPTION’ ... OK
* this is package ‘CNVRanger’ version ‘1.26.0’
* 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 ... ERROR
Running examples in ‘CNVRanger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotEQTL
> ### Title: Plot EQTL region
> ### Aliases: plotEQTL
> 
> ### ** Examples
> 
> 
> # CNV region of interest
> cnvr <- GRanges("chr1:7908902-8336254")
> 
> # Two genes in the neighborhood
> genes <- c("chr1:8021714-8045342:+", "chr1:8412464-8877699:-")
> names(genes) <- c("PARK7", "RERE")
> genes <- GRanges(genes)
> 
> # Annotate differential expression for 1-copy loss
> genes$logFC.CN1 <- c(-0.635, -0.728)
> genes$AdjPValue <- c(8.29e-09, 1.76e-08) 
> 
> # plot
> plotEQTL(cnvr, genes, genome="hg19", cn="CN1")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [genome.ucsc.edu]:
SSL connection timeout
Calls: plotEQTL ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CNVRanger
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘CNVRanger’ ...
** this is package ‘CNVRanger’ version ‘1.26.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (CNVRanger)