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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:alabaster.matrix.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings alabaster.matrix_1.5.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.matrix/DESCRIPTION’ ... OK
* this is package ‘alabaster.matrix’ version ‘1.5.4’
* 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 ‘alabaster.matrix’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘alabaster.matrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: saveDelayedArray
> ### Title: Save DelayedArrays to disk
> ### Aliases: saveDelayedArray stageObject,DelayedArray-method
> ###   stageObject,DelayedMatrix-method saveObject,DelayedArray-method
> 
> ### ** Examples
> 
> mat <- Matrix::rsparsematrix(100, 200, density=0.2)
> rownames(mat) <- paste0("GENE_", seq_len(nrow(mat)))
> dmat <- DelayedArray::DelayedArray(mat) * 1
> 
> dir <- tempfile()
> saveObject(dmat, dir, delayed.preserve.ops=TRUE)
Error: unable to find an inherited method for function ‘nzdata’ for signature ‘x = "SVT_SparseMatrix"’
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    9.             └─alabaster.matrix:::.extract_sparse_details(mat)
   10.               └─DelayedArray::blockApply(...)
   11.                 └─DelayedArray::gridApply(...)
   12.                   └─S4Arrays:::bplapply2(...)
   13.                     ├─BiocGenerics::lapply(X, FUN, ...)
   14.                     └─base::lapply(X, FUN, ...)
   15.                       └─DelayedArray (local) FUN(X[[i]], ...)
   16.                         └─DelayedArray (local) FUN(viewport, ...)
   17.                           └─alabaster.matrix (local) FUN(block, ...)
   18.                             └─SparseArray::nzdata(sparse)
   19.                               └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
  
  [ FAIL 13 | WARN 90 | SKIP 0 | PASS 560 ]
  Error: Test failures
  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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/alabaster.matrix.Rcheck/00check.log’
for details.