##############################################################################
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###
### Running command:
###
###   _R_CHECK_CODETOOLS_PROFILE_="suppressFundefMismatch=TRUE" /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:DelayedArray.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings DelayedArray_0.33.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedArray.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 ‘DelayedArray/DESCRIPTION’ ... OK
* this is package ‘DelayedArray’ version ‘0.33.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'stats4', 'Matrix', 'BiocGenerics', 'MatrixGenerics', 'S4Vectors',
  'IRanges', 'S4Arrays', 'SparseArray'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DelayedArray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DelayedArray-utils.Rd: arbind, acbind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘defaultMultAutoGrids’
Undocumented S4 methods:
  generic '[' and siglist 'DelayedArray,ANY,ANY,ANY'
  generic '[<-' and siglist 'DelayedArray,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ‘DelayedArray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RealizationSink
> ### Title: RealizationSink objects
> ### Aliases: class:RealizationSink RealizationSink-class RealizationSink
> ###   close,RealizationSink-method class:arrayRealizationSink
> ###   arrayRealizationSink-class dim,arrayRealizationSink-method
> ###   write_block,arrayRealizationSink-method
> ###   coerce,arrayRealizationSink,DelayedArray-method AutoRealizationSink
> ###   supportedRealizationBackends registeredRealizationBackends
> ###   getAutoRealizationBackend setAutoRealizationBackend sinkApply
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## USING THE "RealizationSink API": EXAMPLE 1
> ## ---------------------------------------------------------------------
> 
> ## -- STEP 1 --
> ## Create a realization sink. Note that instead of creating a
> ## realization sink by calling a backend-specific sink constructor
> ## (e.g. HDF5Array::HDF5RealizationSink), we set the "automatic
> ## realization backend" to "HDF5Array" and use backend-agnostic
> ## constructor AutoRealizationSink():
> setAutoRealizationBackend("HDF5Array")
> sink <- AutoRealizationSink(c(35L, 50L, 8L))
> dim(sink)
[1] 35 50  8
> 
> ## -- STEP 2 --
> ## Define the grid of viewports to walk on. Here we define a grid made
> ## of very small viewports on 'sink'. Note that, for real-world use cases,
> ## block processing will typically use grids made of much bigger
> ## viewports, usually obtained with defaultSinkAutoGrid().
> ## Also please note that this grid would not be compatible with "linear
> ## write only" realization backends. See "Cross realization backend
> ## compatibility" above in this man page for more information.
> sink_grid <- RegularArrayGrid(dim(sink), spacings=c(20, 20, 4))
> 
> ## -- STEP 3 --
> ## Walk on the grid, and, for each viewport, write random data to it.
> for (bid in seq_along(sink_grid)) {
+     viewport <- sink_grid[[bid]]
+     block <- array(runif(length(viewport)), dim=dim(viewport))
+     sink <- write_block(sink, viewport, block)
+ }
> 
> ## -- An alternative to STEP 3 --
> FUN <- function(sink, viewport) {
+     block <- array(runif(length(viewport)), dim=dim(viewport))
+     write_block(sink, viewport, block)
+ }
> sink <- sinkApply(sink, FUN, grid=sink_grid, verbose=TRUE)
\ processing viewport 1/12 ... ok
\ processing viewport 2/12 ... ok
\ processing viewport 3/12 ... ok
\ processing viewport 4/12 ... ok
\ processing viewport 5/12 ... ok
\ processing viewport 6/12 ... ok
\ processing viewport 7/12 ... ok
\ processing viewport 8/12 ... ok
\ processing viewport 9/12 ... ok
\ processing viewport 10/12 ... ok
\ processing viewport 11/12 ... ok
\ processing viewport 12/12 ... ok
> 
> ## -- STEP 4 --
> ## Close the sink and turn it into a DelayedArray object:
> close(sink)
> A <- as(sink, "DelayedArray")
> A
<35 x 50 x 8> HDF5Array object of type "double":
,,1
            [,1]       [,2]       [,3] ...      [,49]      [,50]
 [1,] 0.09251632 0.73715309 0.57826006   . 0.44599135 0.06597004
 [2,] 0.44674406 0.33379887 0.89571557   . 0.69924371 0.20470113
  ...          .          .          .   .          .          .
[34,]  0.8648171  0.2410861  0.7959126   . 0.90928265 0.03788946
[35,]  0.2427737  0.8570406  0.8277267   . 0.33881426 0.51074875

...

,,8
            [,1]       [,2]       [,3] ...     [,49]     [,50]
 [1,]  0.2475538  0.6427626  0.7057213   . 0.1230515 0.9533773
 [2,]  0.4705060  0.9561530  0.3302344   . 0.6292483 0.4183444
  ...          .          .          .   .         .         .
[34,] 0.69497962 0.56221399 0.40872342   . 0.2511284 0.3580837
[35,] 0.29284090 0.46846839 0.08948379   . 0.1186285 0.8980875

> 
> setAutoRealizationBackend()  # restore default (NULL)
> 
> ## ---------------------------------------------------------------------
> ## USING THE "RealizationSink API": EXAMPLE 2
> ## ---------------------------------------------------------------------
> 
> ## Say we have a 3D array and want to collapse its 3rd dimension by
> ## summing the array elements that are stacked vertically, that is, we
> ## want to compute the matrix M obtained by doing sum(A[i, j, ]) for all
> ## valid i and j. This is very easy to do with an ordinary array:
> collapse_3rd_dim <- function(a) apply(a, MARGIN=1:2, sum)
> 
> ## or, in a slightly more efficient way:
> collapse_3rd_dim <- function(a) {
+     m <- matrix(0, nrow=nrow(a), ncol=ncol(a))
+     for (z in seq_len(dim(a)[[3]]))
+         m <- m + a[ , , z]
+     m
+ }
> 
> ## With a toy 3D array:
> a <- array(runif(8000), dim=c(25, 40, 8))
> dim(collapse_3rd_dim(a))
[1] 25 40
> stopifnot(identical(sum(a), sum(collapse_3rd_dim(a))))  # sanity check
> 
> ## Now say that A is so big that even M wouldn't fit in memory. This is
> ## a situation where we'd want to compute M block by block:
> 
> ## -- STEP 1 --
> ## Create the 2D realization sink:
> setAutoRealizationBackend("HDF5Array")
> sink <- AutoRealizationSink(dim(a)[1:2])
> dim(sink)
[1] 25 40
> 
> ## -- STEP 2 --
> ## Define two grids: one for 'sink' and one for 'a'. Since we're going
> ## to walk on the two grids simultaneously, read a block from 'a' and
> ## write it to 'sink', we need to make sure that we define grids that
> ## are "aligned". More precisely, the two grids must have the same number
> ## of viewports, and the viewports in one must correspond to the viewports
> ## in the other one:
> sink_grid <- colAutoGrid(sink, ncol=10)
> a_spacings <- c(dim(sink_grid[[1L]]), dim(a)[[3]])
> a_grid <- RegularArrayGrid(dim(a), spacings=a_spacings)
> dims(sink_grid)  # dimensions of the individual viewports
     [,1] [,2]
[1,]   25   10
[2,]   25   10
[3,]   25   10
[4,]   25   10
> dims(a_grid)     # dimensions of the individual viewports
     [,1] [,2] [,3]
[1,]   25   10    8
[2,]   25   10    8
[3,]   25   10    8
[4,]   25   10    8
> 
> ## Let's check that our two grids are actually "aligned":
> stopifnot(identical(length(sink_grid), length(a_grid)))
> stopifnot(identical(dims(sink_grid), dims(a_grid)[ , 1:2, drop=FALSE]))
> 
> ## -- STEP 3 --
> ## Walk on the two grids simultaneously:
> for (bid in seq_along(sink_grid)) {
+     ## Read block from 'a'.
+     a_viewport <- a_grid[[bid]]
+     block <- read_block(a, a_viewport)
+     ## Collapse it.
+     block <- collapse_3rd_dim(block)
+     ## Write the collapsed block to 'sink'.
+     sink_viewport <- sink_grid[[bid]]
+     sink <- write_block(sink, sink_viewport, block)
+ }
> 
> ## -- An alternative to STEP 3 --
> FUN <- function(sink, sink_viewport) {
+     ## Read block from 'a'.
+     bid <- currentBlockId()
+     a_viewport <- a_grid[[bid]]
+     block <- read_block(a, a_viewport)
+     ## Collapse it.
+     block <- collapse_3rd_dim(block)
+     ## Write the collapsed block to 'sink'.
+     write_block(sink, sink_viewport, block)
+ }
> sink <- sinkApply(sink, FUN, grid=sink_grid, verbose=TRUE)
\ processing viewport 1/4 ... ok
\ processing viewport 2/4 ... ok
\ processing viewport 3/4 ... ok
\ processing viewport 4/4 ... ok
> 
> ## -- STEP 4 --
> ## Close the sink and turn it into a DelayedArray object:
> close(sink)
> M <- as(sink, "DelayedArray")
> M
<25 x 40> HDF5Matrix object of type "double":
          [,1]     [,2]     [,3] ...    [,39]    [,40]
 [1,] 3.605488 4.428343 3.515007   . 4.490627 3.567119
 [2,] 3.971004 2.981488 4.022526   . 2.996765 4.582575
 [3,] 3.644131 5.740389 3.919445   . 3.321812 4.778346
 [4,] 5.481778 3.556413 3.578300   . 3.204930 3.513076
 [5,] 3.255126 5.320396 4.631426   . 3.684879 3.591320
  ...        .        .        .   .        .        .
[21,] 3.979501 3.753845 4.779659   . 4.557505 3.786337
[22,] 2.799614 4.675706 4.166002   . 4.272493 3.825482
[23,] 5.047167 5.156586 3.834504   . 5.014369 4.585006
[24,] 4.857444 3.110475 4.105436   . 2.845470 4.476643
[25,] 4.229303 3.589894 3.714495   . 2.814014 4.124024
> 
> ## Sanity check:
> stopifnot(identical(collapse_3rd_dim(a), as.array(M)))
> 
> setAutoRealizationBackend()  # restore default (NULL)
> 
> ## ---------------------------------------------------------------------
> ## USING THE "RealizationSink API": AN ADVANCED EXAMPLE
> ## ---------------------------------------------------------------------
> 
> ## Say we have 2 matrices with the same number of columns. Each column
> ## represents a biological sample:
> library(HDF5Array)
Loading required package: h5mread
Loading required package: rhdf5

Attaching package: ‘h5mread’

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

    h5ls

> R <- as(matrix(runif(75000), ncol=1000), "HDF5Array")   # 75 rows
> G <- as(matrix(runif(250000), ncol=1000), "HDF5Array")  # 250 rows
> 
> ## Say we want to compute the matrix U obtained by applying the same
> ## binary functions FUN() to all samples i.e. U is defined as:
> ##
> ##   U[ , j] <- FUN(R[ , j], G[ , j]) for 1 <= j <= 1000
> ##
> ## Note that FUN() should return a vector of constant length, say 200,
> ## so U will be a 200x1000 matrix. A naive implementation would be:
> ##
> ##   pFUN <- function(r, g) {
> ##       stopifnot(ncol(r) == ncol(g))  # sanity check
> ##       sapply(seq_len(ncol(r)), function(j) FUN(r[ , j], g[ , j]))
> ##   }
> ##
> ## But because U is going to be too big to fit in memory, we can't
> ## just do pFUN(R, G). So we want to compute U block by block and
> ## write the blocks to disk as we go. The blocks will be made of full
> ## columns. Also since we need to walk on 2 matrices at the same time
> ## (R and G), we can't use blockApply() or blockReduce() so we'll use
> ## a "for" loop.
> 
> ## Before we get to the "for" loop, we need 4 things:
> 
> ## 1. Two grids of blocks, one on R and one on G. The blocks in the
> ##    two grids must contain the same number of columns. We arbitrarily
> ##    choose to use blocks of 150 columns:
> R_grid <- colAutoGrid(R, ncol=150)
> G_grid <- colAutoGrid(G, ncol=150)
> 
> ## 2. The function pFUN(). It will take 2 blocks as input, 1 from R
> ##    and 1 from G, apply FUN() to all the samples in the blocks,
> ##    and return a matrix with one columns per sample:
> pFUN <- function(r, g) {
+     stopifnot(ncol(r) == ncol(g))  # sanity check
+     ## Return a matrix with 200 rows with random values. Completely
+     ## artificial sorry. A realistic example would actually need to
+     ## apply the same binary function to r[ ,j] and g[ , j] for
+     ## 1 <= j <= ncol(r).
+     matrix(runif(200 * ncol(r)), nrow=200)
+ }
> 
> ## 3. A RealizationSink derivative where to write the matrices returned
> ##    by pFUN() as we go:
> setAutoRealizationBackend("HDF5Array")
> U_sink <- AutoRealizationSink(c(200L, 1000L))
> 
> ## 4. Finally, we create a grid on U_sink with viewports that contain
> ##    the same number of columns as the corresponding blocks in R and G:
> U_grid <- colAutoGrid(U_sink, ncol=150)
> 
> ## Note that the three grids should have the same number of viewports:
> stopifnot(length(U_grid) == length(R_grid))
> stopifnot(length(U_grid) == length(G_grid))
> 
> ## 5. Now we can proceed. We use a "for" loop to walk on R and G
> ##    simultaneously, block by block, apply pFUN(), and write the
> ##    output of pFUN() to U_sink:
> for (bid in seq_along(U_grid)) {
+     R_block <- read_block(R, R_grid[[bid]])
+     G_block <- read_block(G, G_grid[[bid]])
+     U_block <- pFUN(R_block, G_block)
+     U_sink <- write_block(U_sink, U_grid[[bid]], U_block)
+ }
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
> 
> ## An alternative to the "for" loop is to use sinkApply():
> FUN <- function(U_sink, U_viewport) {
+     bid <- currentBlockId()
+     R_block <- read_block(R, R_grid[[bid]])
+     G_block <- read_block(G, G_grid[[bid]])
+     U_block <- pFUN(R_block, G_block)
+     write_block(U_sink, U_viewport, U_block)
+ }
> U_sink <- sinkApply(U_sink, FUN, grid=U_grid, verbose=TRUE)
\ processing viewport 1/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 2/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 3/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 4/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 5/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 6/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
\ processing viewport 7/7 ... Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
ok
> 
> close(U_sink)
> U <- as(U_sink, "DelayedArray")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'seed' in selecting a method for function 'DelayedArray': H5Dread() returned an error
Calls: as ... .read_h5dataset_first_val -> h5mread -> .Call2 -> .handleSimpleError -> h
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DelayedMatrix-rowsum 10.283  1.401  15.738
DelayedArray-utils    7.344  0.132  11.009
DelayedArray-class    5.833  0.204  12.179
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* 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, 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/DelayedArray.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL DelayedArray
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘DelayedArray’ ...
** this is package ‘DelayedArray’ version ‘0.33.6’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c compress_atomic_vector.c -o compress_atomic_vector.o
gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘sweep’ in package ‘DelayedArray’
Creating a new generic function for ‘scale’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DelayedArray)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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.

> require("DelayedArray") || stop("unable to load DelayedArray package")
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

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

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

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

[1] TRUE
> DelayedArray:::.test()
Error in S4Arrays:::normarg_perm(perm, dim(seed)) : 
  'perm' must be an integer vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    'perm' cannot be an empty vector
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions with an extent of 1 can be dropped
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    all non-NA values in 'perm' must be >= 1 and <= 'length(dim(a))'
Error in validObject(.Object) : invalid class "DelayedAperm" object: 
    only dimensions with an extent of 1 can be dropped
Loading required package: h5mread
Loading required package: rhdf5

Attaching package: 'h5mread'

The following object is masked from 'package:rhdf5':

    h5ls

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array

Loading required namespace: HDF5Array


Attaching package: 'genefilter'

The following object is masked from 'package:DelayedArray':

    rowVars

The following objects are masked from 'package:SparseArray':

    rowSds, rowVars

The following objects are masked from 'package:MatrixGenerics':

    rowSds, rowVars

The following objects are masked from 'package:matrixStats':

    rowSds, rowVars

Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at the
  moment. Note that you can check the number of seeds with nseed(). You can use
  'seedApply(x, identity)' to extract all the seeds as a list.
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced
Error : unable to find an inherited method for function 'is_noop' for signature 'x = "DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at the
  moment. Note that you can check the number of seeds with nseed(). You can use
  'seedApply(x, identity)' to extract all the seeds as a list.
Error : unable to find an inherited method for function 'is_noop' for signature 'x = "DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at the
  moment. Note that you can check the number of seeds with nseed(). You can use
  'seedApply(x, identity)' to extract all the seeds as a list.
Error : unable to find an inherited method for function 'is_noop' for signature 'x = "DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at the
  moment. Note that you can check the number of seeds with nseed(). You can use
  'seedApply(x, identity)' to extract all the seeds as a list.
Error : unable to find an inherited method for function 'is_noop' for signature 'x = "DelayedNaryIsoOp"'
Error in seed(x) : 
  seed() is not supported on a DelayedArray object with multiple seeds at the
  moment. Note that you can check the number of seeds with nseed(). You can use
  'seedApply(x, identity)' to extract all the seeds as a list.
Error : unable to find an inherited method for function 'is_noop' for signature 'x = "DelayedNaryIsoOp"'
Error in match.fun(OP) : 'NULL' is not a function, character or symbol
Error in match.fun(OP) : 
  'list(NULL)' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found
Error in new_DelayedNaryIsoOp("<=", array(dim = 4:2), array(dim = 2:4)) : 
  non-conformable array-like objects
Error in S4Arrays:::normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must be NULL or a list
Error in S4Arrays:::normarg_dimnames(dimnames, seed_dim) : 
  the supplied 'dimnames' must have one list element per dimension
Error in FUN(X[[i]], ...) : 
  each list element in the supplied 'dimnames' must be NULL or a character
  vector
Error in FUN(X[[i]], ...) : 
  length of 'dimnames[[1]]' (26) must equal the array extent (5)
Error in S4Arrays:::normalize_Nindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error in S4Arrays:::normalize_Nindex(Nindex, seed) : 
  'Nindex' must be a list with one list element per dimension in 'x'
Error : subscript contains out-of-bounds indices
Error : subscript contains invalid names
Error : subscript contains out-of-bounds ranges
Error : subscript contains out-of-bounds ranges
Error in new_DelayedUnaryIsoOpStack(.TEST_SVT3, NULL) : 
  'OPS' must be a list
Error in FUN(X[[i]], ...) : 
  'OPS[[1L]]' is not a function, character or symbol
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'not-an-existing-function' of mode 'function' was not found


RUNIT TEST PROTOCOL -- Sun Apr  6 19:45:23 2025 
*********************************************** 
Number of test functions: 43 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
DelayedArray RUnit Tests - 43 test functions, 0 errors, 0 failures
Number of test functions: 43 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
709.516   5.453 995.541