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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:corral.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings corral_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/corral.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 ‘corral/DESCRIPTION’ ... OK
* this is package ‘corral’ version ‘1.19.0’
* 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 ‘corral’ 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: ‘ggthemes:::check_pal_n’
  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
biplot_corral: no visible binding for global variable ‘Name’
plot_embedding: no visible binding for global variable ‘Xdim’
plot_embedding: no visible binding for global variable ‘Ydim’
scal_var: no visible binding for global variable ‘PC_ind’
scal_var: no visible binding for global variable ‘sv’
scal_var: no visible binding for global variable ‘Batch’
Undefined global functions or variables:
  Batch Name PC_ind Xdim Ydim sv
* checking Rd files ... NOTE
prepare_Rd: corral_preproc.Rd:41-43: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corral.Rd: SingleCellExperiment
  corralm.Rd: SingleCellExperiment
  plot_embedding.Rd: ggplot2
  plot_embedding_sce.Rd: SingleCellExperiment, ggplot2
  scal_var.Rd: ggplot2
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
biplot_corral          58.607  7.414  66.187
add_embeddings2scelist 10.634  2.102  13.075
corral                 10.320  1.945  12.517
corralm                 9.753  1.922  11.956
plot_embedding_sce      5.739  1.222   7.092
sce2matlist             4.999  1.093   6.194
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 ‘corral_dimred.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/corral.Rcheck/vign_test/corral/vignettes/corral_dimred_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/corral.Rcheck/vign_test/corral/vignettes/corral_dimred_files/figure-html/unnamed-chunk-5-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/corral.Rcheck/vign_test/corral/vignettes/corral_dimred_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/corral.Rcheck/vign_test/corral/vignettes/corral_dimred_files/figure-html/unnamed-chunk-10-1.png" but not available.
--- finished re-building ‘corral_dimred.Rmd’

--- re-building ‘corralm_alignment.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from corralm_alignment.Rmd:45-54 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. ├─CellBench::load_all_data()
  2. │ ├─BiocGenerics::updateObject(sc_10x)
  3. │ └─SingleCellExperiment::updateObject(sc_10x)
  4. │   ├─methods::callNextMethod()
  5. │   └─SummarizedExperiment (local) .nextMethod(object = object)
  6. │     ├─BiocGenerics::updateObject(object@rowRanges, ..., verbose = verbose)
  7. │     └─GenomicRanges::updateObject(object@rowRanges, ..., verbose = verbose)
  8. │       ├─BiocGenerics::updateObject(object@unlistData, ..., verbose = verbose)
  9. │       └─GenomicRanges::updateObject(object@unlistData, ..., verbose = verbose)
 10. │         └─BiocGenerics::updateObject(object@seqinfo, ..., verbose = verbose)
 11. └─methods:::.extendsForS3(`<chr>`)
 12.   └─methods::extends(Class, maybe = FALSE)
 13.     └─methods::getClassDef(class1)
 14.       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'corralm_alignment.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘corralm_alignment.Rmd’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/corral.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL corral
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘corral’ ...
** this is package ‘corral’ version ‘1.19.0’
** 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 (corral)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> proc.time()
   user  system elapsed 
  0.143   0.032   0.164