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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings BiocGenerics_0.53.6.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/BiocGenerics.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.53.6’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘graphics’ ‘stats’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... WARNING
Missing link(s) in Rd file 'as.data.frame.Rd':
  ‘[IRanges]{as.data.frame,IntegerRanges-method}’

Missing link(s) in Rd file 'order.Rd':
  ‘[IRanges]{order,IntegerRanges-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 examples ... ERROR
Running examples in ‘BiocGenerics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: containsOutOfMemoryData
> ### Title: Does an object contain out-of-memory data?
> ### Aliases: containsOutOfMemoryData containsOutOfMemoryData,ANY-method
> ###   containsOutOfMemoryData,list-method
> ###   containsOutOfMemoryData,environment-method class:OutOfMemoryObject
> ###   OutOfMemoryObject-class OutOfMemoryObject
> ###   containsOutOfMemoryData,OutOfMemoryObject-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> containsOutOfMemoryData
standardGeneric for "containsOutOfMemoryData" defined from package "BiocGenerics"

function (object) 
standardGeneric("containsOutOfMemoryData")
<bytecode: 0x59fb1129e9a0>
<environment: 0x59fb102a0d38>
Methods may be defined for arguments: object
Use  showMethods(containsOutOfMemoryData)  for currently available ones.
> showMethods("containsOutOfMemoryData")
Function: containsOutOfMemoryData (package BiocGenerics)
object="ANY"
object="OutOfMemoryObject"
object="environment"
object="list"

> 
> ## The default method:
> selectMethod("containsOutOfMemoryData", "ANY")
Method Definition:

function (object) 
{
    if (isS4(object)) 
        return(.S4_object_contains_out_of_memory_data(object))
    FALSE
}
<bytecode: 0x59fb112a1f20>
<environment: namespace:BiocGenerics>

Signatures:
        object
target  "ANY" 
defined "ANY" 
> 
> ## The method for list objects:
> selectMethod("containsOutOfMemoryData", "list")
Method Definition:

function (object) 
{
    for (x in object) {
        if (containsOutOfMemoryData(x)) 
            return(TRUE)
    }
    FALSE
}
<bytecode: 0x59fb112a47e0>
<environment: namespace:BiocGenerics>

Signatures:
        object
target  "list"
defined "list"
> 
> ## The method for OutOfMemoryObject derivatives:
> selectMethod("containsOutOfMemoryData", "OutOfMemoryObject")
Method Definition:

function (object) 
TRUE
<bytecode: 0x59fb112a54c8>
<environment: namespace:BiocGenerics>

Signatures:
        object             
target  "OutOfMemoryObject"
defined "OutOfMemoryObject"
> 
> m <- matrix(0, nrow=7, ncol=10)
> m[sample(length(m), 20)] <- runif(20)
> containsOutOfMemoryData(m)  # FALSE
[1] FALSE
> 
> library(SparseArray)
Loading required package: Matrix
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:Matrix’:

    expand, unname

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: S4Arrays
Loading required package: abind
Loading required package: IRanges

Attaching package: ‘S4Arrays’

The following object is masked from ‘package:abind’:

    abind

The following object is masked from ‘package:base’:

    rowsum

> svt <- as(m, "SparseArray")
> svt
<7 x 10 SparseMatrix> of type "double" [nzcount=20 (29%)]:
          [,1]      [,2]      [,3] ...      [,9]     [,10]
[1,] 0.0000000 0.0000000 0.0000000   . 0.0000000 0.7176185
[2,] 0.0000000 0.0000000 0.0000000   . 0.0000000 0.0000000
[3,] 0.0000000 0.6607978 0.0000000   . 0.3841037 0.0000000
[4,] 0.0000000 0.0000000 0.0000000   . 0.0000000 0.7698414
[5,] 0.0000000 0.0000000 0.0000000   . 0.0000000 0.0000000
[6,] 0.9446753 0.0000000 0.1765568   . 0.0000000 0.0000000
[7,] 0.0000000 0.0000000 0.0000000   . 0.0000000 0.3721239
> containsOutOfMemoryData(m)  # FALSE
[1] FALSE
> containsOutOfMemoryData(list(m, svt))  # FALSE
[1] FALSE
> 
> library(HDF5Array)
Loading required package: DelayedArray

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:base’:

    apply, scale, sweep

Loading required package: h5mread
Loading required package: rhdf5

Attaching package: ‘h5mread’

The following object is masked from ‘package:rhdf5’:

    h5ls

Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: package or namespace load failed for ‘HDF5Array’:
 .onLoad failed in loadNamespace() for 'HDF5Array', details:
  call: .set_dump_dir(dir)
  error: cannot create directory "/tmp/Rtmplcu6ML/HDF5Array_dump"
Execution halted
* checking for unstated dependencies in ‘tests’ ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking tests ...Fatal error: cannot create 'R_TempDir'
 ERROR
* checking PDF version of manual ... ERROR
Rd conversion errors:
Warning in file(outfile, "wt") :
  cannot open file '/tmp/Rtmplzot7s/Rd2pdf95f6a25c3e633/Rd2.tex': No such file or directory
Error in file(outfile, "wt") : cannot open the connection
* DONE

Status: 3 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/BiocGenerics.Rcheck/00check.log’
for details.