##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
 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             17.412  1.451  30.261
plotRecurrentRegions 14.146  0.599  17.475
plotManhattan         5.651  0.425   6.076
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘CNVRanger.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/CNVRanger.Rcheck/vign_test/CNVRanger/vignettes/CNVRanger_files/figure-html/recurrViz-1.png" but not available.

Quitting from CNVRanger.Rmd:407-412 [getBtGenes]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
---
Backtrace:
    ▆
 1. └─AnnotationHub::AnnotationHub()
 2.   └─AnnotationHub::.Hub(...)
 3.     └─base::tryCatch(...)
 4.       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 5.         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6.           └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CNVRanger.Rmd' failed with diagnostics:
failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
--- failed re-building ‘CNVRanger.Rmd’

SUMMARY: processing the following file failed:
  ‘CNVRanger.Rmd’

Error: Vignette re-building failed.
Execution halted

* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CNVRanger
###
##############################################################################
##############################################################################


* 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)