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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings S4Arrays_1.7.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Arrays.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘S4Arrays/DESCRIPTION’ ... OK
* this is package ‘S4Arrays’ version ‘1.7.3’
* 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 ‘S4Arrays’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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:
  extract_array.Rd: dgCMatrix-class
  is_sparse.Rd: dgCMatrix-class
  read_block.Rd: dgCMatrix-class, lgCMatrix-class
  type.Rd: dgCMatrix-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 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 ‘S4Arrays-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: array_recycling
> ### Title: Multidimensional array recycling
> ### Aliases: array_recycling class:tile tile-class tile as_tile
> ###   Ops,array,tile-method Ops,tile,array-method Ops,tile,tile-method
> ### Keywords: array methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## 2D EXAMPLES
> ## ---------------------------------------------------------------------
> m0 <- matrix(1:54, nrow=6)
> x <- c(-1, 0, 100)
> 
> ## Arithmetic operations in base R recycle 'x' along the first dimension
> ## of the matrix ("vertical recycling"):
> m0 * x
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,]   -1   -7  -13  -19  -25  -31  -37  -43  -49
[2,]    0    0    0    0    0    0    0    0    0
[3,]  300  900 1500 2100 2700 3300 3900 4500 5100
[4,]   -4  -10  -16  -22  -28  -34  -40  -46  -52
[5,]    0    0    0    0    0    0    0    0    0
[6,]  600 1200 1800 2400 3000 3600 4200 4800 5400
> 
> ## To recycle 'x' along the second dimension of the matrix ("horizontal
> ## recycling"), we turn it into an "horizontal" tile:
> t <- as_tile(x, along=2)
> t
An object of class "tile"
     [,1] [,2] [,3]
[1,]   -1    0  100
> 
> m0 * t
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9]
[1,]   -1    0 1300  -19    0 3100  -37    0 4900
[2,]   -2    0 1400  -20    0 3200  -38    0 5000
[3,]   -3    0 1500  -21    0 3300  -39    0 5100
[4,]   -4    0 1600  -22    0 3400  -40    0 5200
[5,]   -5    0 1700  -23    0 3500  -41    0 5300
[6,]   -6    0 1800  -24    0 3600  -42    0 5400
> 
> ## The above produces the same result as the double-transposition trick
> ## but is more efficient (and also makes code easier to read):
> stopifnot(identical(m0 * t, t(t(m0) * x)))
> 
> ## A less artificial example:
> cs0 <- colSums(m0)
> m <- m0 / as_tile(cs0, along=2)
> 
> stopifnot(all(colSums(m) == 1))  # sanity check
Error: all(colSums(m) == 1) is not TRUE
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Array-kronecker-methods 4.909  0.133   5.051
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/S4Arrays.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL S4Arrays
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘S4Arrays’ ...
** this is package ‘S4Arrays’ version ‘1.7.3’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_S4Arrays.c -o R_init_S4Arrays.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c abind.c -o abind.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c array_selection.c -o array_selection.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c dim_tuning_utils.c -o dim_tuning_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rowsum.c -o rowsum.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-S4Arrays/00new/S4Arrays/libs
** R
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’
Creating a new generic function for ‘abind’ in package ‘S4Arrays’
** 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 (S4Arrays)

R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

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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.

> library(testthat)
> library(S4Arrays)
Loading required package: Matrix
Loading required package: abind
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: 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: IRanges

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

> 
> test_check("S4Arrays")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 514 ]
> 
> proc.time()
   user  system elapsed 
 10.521   0.166  10.707