##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:S4Arrays.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings S4Arrays_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/S4Arrays.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-07 08:58:44 UTC
* checking for file ‘S4Arrays/DESCRIPTION’ ... OK
* this is package ‘S4Arrays’ version ‘1.11.1’
* 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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:
  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 ... INFO
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-kronecker-methods
> ### Title: Kronecker products on Array objects
> ### Aliases: Array-kronecker-methods Array_kronecker-methods
> ###   Array-kronecker Array_kronecker kronecker kronecker,Array,ANY-method
> ###   kronecker,ANY,Array-method kronecker,Array,Array-method kronecker2
> ### Keywords: array methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## SIMPLE kronecker2() EXAMPLES
> ## ---------------------------------------------------------------------
> 
> m1 <- matrix(1:10, nrow=2)     # 2 x 5 matrix
> m2 <- matrix(101:106, nrow=3)  # 3 x 2 matrix
> kronecker2(m1, m2)             # 6 x 10 matrix
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,]  101  104  303  312  505  520  707  728  909   936
[2,]  102  105  306  315  510  525  714  735  918   945
[3,]  103  106  309  318  515  530  721  742  927   954
[4,]  202  208  404  416  606  624  808  832 1010  1040
[5,]  204  210  408  420  612  630  816  840 1020  1050
[6,]  206  212  412  424  618  636  824  848 1030  1060
> 
> a1 <- array(1:16, dim=c(4, 2, 2))
> a2 <- array(1:30, dim=c(3, 5, 2))
> kronecker2(a1, a2)    # 12 x 10 x 4 array
, , 1

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    1    4    7   10   13    5   20   35   50    65
 [2,]    2    5    8   11   14   10   25   40   55    70
 [3,]    3    6    9   12   15   15   30   45   60    75
 [4,]    2    8   14   20   26    6   24   42   60    78
 [5,]    4   10   16   22   28   12   30   48   66    84
 [6,]    6   12   18   24   30   18   36   54   72    90
 [7,]    3   12   21   30   39    7   28   49   70    91
 [8,]    6   15   24   33   42   14   35   56   77    98
 [9,]    9   18   27   36   45   21   42   63   84   105
[10,]    4   16   28   40   52    8   32   56   80   104
[11,]    8   20   32   44   56   16   40   64   88   112
[12,]   12   24   36   48   60   24   48   72   96   120

, , 2

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]   16   19   22   25   28   80   95  110  125   140
 [2,]   17   20   23   26   29   85  100  115  130   145
 [3,]   18   21   24   27   30   90  105  120  135   150
 [4,]   32   38   44   50   56   96  114  132  150   168
 [5,]   34   40   46   52   58  102  120  138  156   174
 [6,]   36   42   48   54   60  108  126  144  162   180
 [7,]   48   57   66   75   84  112  133  154  175   196
 [8,]   51   60   69   78   87  119  140  161  182   203
 [9,]   54   63   72   81   90  126  147  168  189   210
[10,]   64   76   88  100  112  128  152  176  200   224
[11,]   68   80   92  104  116  136  160  184  208   232
[12,]   72   84   96  108  120  144  168  192  216   240

, , 3

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]    9   36   63   90  117   13   52   91  130   169
 [2,]   18   45   72   99  126   26   65  104  143   182
 [3,]   27   54   81  108  135   39   78  117  156   195
 [4,]   10   40   70  100  130   14   56   98  140   182
 [5,]   20   50   80  110  140   28   70  112  154   196
 [6,]   30   60   90  120  150   42   84  126  168   210
 [7,]   11   44   77  110  143   15   60  105  150   195
 [8,]   22   55   88  121  154   30   75  120  165   210
 [9,]   33   66   99  132  165   45   90  135  180   225
[10,]   12   48   84  120  156   16   64  112  160   208
[11,]   24   60   96  132  168   32   80  128  176   224
[12,]   36   72  108  144  180   48   96  144  192   240

, , 4

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,]  144  171  198  225  252  208  247  286  325   364
 [2,]  153  180  207  234  261  221  260  299  338   377
 [3,]  162  189  216  243  270  234  273  312  351   390
 [4,]  160  190  220  250  280  224  266  308  350   392
 [5,]  170  200  230  260  290  238  280  322  364   406
 [6,]  180  210  240  270  300  252  294  336  378   420
 [7,]  176  209  242  275  308  240  285  330  375   420
 [8,]  187  220  253  286  319  255  300  345  390   435
 [9,]  198  231  264  297  330  270  315  360  405   450
[10,]  192  228  264  300  336  256  304  352  400   448
[11,]  204  240  276  312  348  272  320  368  416   464
[12,]  216  252  288  324  360  288  336  384  432   480

> 
> ## The Kronecker product is **not** commutative:
> m1 <- matrix(LETTERS[1:10], nrow=2)
> m2 <- matrix(letters[1:6], nrow=3)
> kronecker2(m1, m2, paste, sep="*")
     [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9]  [,10]
[1,] "A*a" "A*d" "C*a" "C*d" "E*a" "E*d" "G*a" "G*d" "I*a" "I*d"
[2,] "A*b" "A*e" "C*b" "C*e" "E*b" "E*e" "G*b" "G*e" "I*b" "I*e"
[3,] "A*c" "A*f" "C*c" "C*f" "E*c" "E*f" "G*c" "G*f" "I*c" "I*f"
[4,] "B*a" "B*d" "D*a" "D*d" "F*a" "F*d" "H*a" "H*d" "J*a" "J*d"
[5,] "B*b" "B*e" "D*b" "D*e" "F*b" "F*e" "H*b" "H*e" "J*b" "J*e"
[6,] "B*c" "B*f" "D*c" "D*f" "F*c" "F*f" "H*c" "H*f" "J*c" "J*f"
> kronecker2(m2, m1, paste, sep="*")
     [,1]  [,2]  [,3]  [,4]  [,5]  [,6]  [,7]  [,8]  [,9]  [,10]
[1,] "a*A" "a*C" "a*E" "a*G" "a*I" "d*A" "d*C" "d*E" "d*G" "d*I"
[2,] "a*B" "a*D" "a*F" "a*H" "a*J" "d*B" "d*D" "d*F" "d*H" "d*J"
[3,] "b*A" "b*C" "b*E" "b*G" "b*I" "e*A" "e*C" "e*E" "e*G" "e*I"
[4,] "b*B" "b*D" "b*F" "b*H" "b*J" "e*B" "e*D" "e*F" "e*H" "e*J"
[5,] "c*A" "c*C" "c*E" "c*G" "c*I" "f*A" "f*C" "f*E" "f*G" "f*I"
[6,] "c*B" "c*D" "c*F" "c*H" "c*J" "f*B" "f*D" "f*F" "f*H" "f*J"
> 
> ## Sanity checks:
> stopifnot(
+   identical(kronecker2(m1, m2, paste0), kronecker(m1, m2, paste0)),
+   identical(kronecker2(m2, m1, paste0), kronecker(m2, m1, paste0))
+ )
> 
> ## ---------------------------------------------------------------------
> ## USING kronecker() ON Array DERIVATIVES
> ## ---------------------------------------------------------------------
> ## The user should typically avoid direct calls to kronecker2() and
> ## stick to kronecker(). Because this is a generic function, it will
> ## dispatch to the appropriate method based on the classes of the input
> ## objects. If one of them is an Array derivative, kronecker2() will
> ## be called thanks to the methods defined in the S4Arrays package and
> ## listed in the Usage section above.
> 
> ## With SparseMatrix objects (Array derivatives):
> library(SparseArray)
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

> sm1 <- poissonSparseMatrix(300, 15, density=0.25)
> sm2 <- poissonSparseMatrix(80, 500, density=0.15)
> kronecker2(sm1, sm2)  # 24000 x 7500 SparseMatrix object
<24000 x 7500 SparseMatrix> of type "integer" [nzcount=6996840 (3.9%)]:
            [,1]    [,2]    [,3]    [,4] ... [,7497] [,7498] [,7499] [,7500]
    [1,]       0       0       0       0   .       0       0       0       0
    [2,]       0       0       0       0   .       0       0       0       0
    [3,]       0       0       0       0   .       0       0       0       0
    [4,]       0       0       0       0   .       0       0       0       0
    [5,]       0       0       0       0   .       0       0       0       0
     ...       .       .       .       .   .       .       .       .       .
[23996,]       1       0       0       0   .       0       0       0       0
[23997,]       2       0       0       0   .       0       0       0       0
[23998,]       0       0       0       1   .       0       0       0       0
[23999,]       0       0       2       0   .       0       0       0       0
[24000,]       0       0       1       0   .       0       0       0       0
> 
> ## With TENxMatrix objects (DelayedArray derivatives, therefore also
> ## Array derivatives):
> 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

> M1 <- writeTENxMatrix(sm1)  # 300 x 15 TENxMatrix object

 *** caught segfault ***
address 0xffffffff910ccb98, cause 'memory not mapped'

Traceback:
 1: .Call2("C_h5mread", filepath, name, starts, counts, noreduce,     as.vector, as.integer, as.sparse, method, use.H5Dread_chunk,     PACKAGE = "h5mread")
 2: h5mread(filepath, name, starts = list(old_len), as.vector = TRUE)
 3: .append_indptr(sink@filepath, sink@group, block_indptr)
 4: write_block(sink, viewport, block)
 5: write_block(sink, viewport, block)
 6: FUN(init, viewport, ...)
 7: FUN(viewport, init, ...)
 8: gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
 9: sinkApply(sink, FUN, x, verbose, verbose_read_block, grid = grid,     verbose = FALSE)
10: BLOCK_write_to_sink(sink, x, verbose = verbose)
11: writeTENxMatrix(sm1)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/S4Arrays.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL S4Arrays
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘S4Arrays’ ...
** this is package ‘S4Arrays’ version ‘1.11.1’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c R_init_S4Arrays.c -o R_init_S4Arrays.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/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 -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c abind.c -o abind.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c array_selection.c -o array_selection.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c dim_tuning_utils.c -o dim_tuning_utils.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c rowsum.c -o rowsum.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

> 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")
Warning: stack imbalance in '::', 79 then 81
Warning: stack imbalance in '<-', 77 then 79
Warning: stack imbalance in '{', 73 then 75
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 514 ]
> 
> proc.time()
   user  system elapsed 
 36.306   0.855  37.155