##############################################################################
##############################################################################
###
### 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: DelayedArray-class
> ### Title: DelayedArray objects
> ### Aliases: class:DelayedArray DelayedArray-class class:DelayedMatrix
> ###   DelayedMatrix-class DelayedMatrix
> ###   coerce,DelayedArray,DelayedMatrix-method
> ###   coerce,DelayedMatrix,DelayedArray-method dim,DelayedArray-method
> ###   dimnames,DelayedArray-method extract_array,DelayedArray-method
> ###   new_DelayedArray DelayedArray DelayedArray,ANY-method
> ###   DelayedArray,DelayedArray-method DelayedArray,DelayedOp-method
> ###   class:DelayedArray1 DelayedArray1-class DelayedArray1
> ###   updateObject,DelayedArray-method type aperm.DelayedArray
> ###   aperm,DelayedArray-method dim<-,DelayedArray-method
> ###   dimnames<-,DelayedArray,ANY-method names,DelayedArray-method
> ###   names<-,DelayedArray-method drop,DelayedArray-method
> ###   [,DelayedArray-method [<-,DelayedArray-method
> ###   coerce,DelayedArray,SparseArraySeed-method
> ###   coerce,DelayedArray,COO_SparseArray-method [[,DelayedArray-method
> ###   show,DelayedArray-method c,DelayedArray-method
> ###   splitAsList,DelayedArray-method split.DelayedArray
> ###   split,DelayedArray,ANY-method matrixClass
> ###   matrixClass,DelayedArray-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. WRAP AN ORDINARY ARRAY IN A DelayedArray OBJECT
> ## ---------------------------------------------------------------------
> a <- array(runif(1500000), dim=c(10000, 30, 5))
> A <- DelayedArray(a)
> A
<10000 x 30 x 5> DelayedArray object of type "double":
,,1
               [,1]       [,2]       [,3] ...     [,29]     [,30]
    [1,] 0.26550866 0.06471249 0.21060275   . 0.5984631 0.3642249
    [2,] 0.37212390 0.67661240 0.11478638   . 0.3827384 0.3018117
     ...          .          .          .   .         .         .
 [9999,] 0.56811624 0.60156001 0.07323793   . 0.4622780 0.5157081
[10000,] 0.65267704 0.11131752 0.34135877   . 0.1236884 0.3565323

...

,,5
               [,1]       [,2]       [,3] ...      [,29]      [,30]
    [1,] 0.54129409 0.03796528 0.42452018   . 0.85943698 0.98683725
    [2,] 0.60637103 0.41651787 0.26198322   . 0.05140486 0.31275299
     ...          .          .          .   .          .          .
 [9999,] 0.45527560 0.38282105 0.06664536   .  0.7054346  0.2747098
[10000,] 0.47353445 0.72197082 0.57871223   .  0.7802741  0.8555813

> ## The seed of a DelayedArray object is **always** treated as a
> ## "read-only" object so will never be modified by the operations
> ## we perform on A:
> stopifnot(identical(a, seed(A)))
> type(A)
[1] "double"
> 
> ## N-dimensional single bracket subsetting:
> m <- a[11:20 , 5, -3]  # an ordinary matrix
> M <- A[11:20 , 5, -3]  # a DelayedMatrix object
> stopifnot(identical(m, as.array(M)))
> 
> ## 1D-style single bracket subsetting:
> A[11:20]
 [1] 0.2059746 0.1765568 0.6870228 0.3841037 0.7698414 0.4976992 0.7176185
 [8] 0.9919061 0.3800352 0.7774452
> A[A <= 1e-5]
 [1] 8.431729e-06 3.895489e-06 8.556060e-06 2.781628e-06 1.548324e-07
 [6] 5.243346e-07 6.905291e-06 1.089182e-06 7.419847e-06 8.758856e-06
[11] 9.631272e-06 4.038448e-06 4.681293e-06 1.522014e-06 3.511552e-06
[16] 9.462470e-06
> stopifnot(identical(a[a <= 1e-5], A[A <= 1e-5]))
> 
> ## Subassignment:
> A[A < 0.2] <- NA
> a[a < 0.2] <- NA
> stopifnot(identical(a, as.array(A)))
> 
> A[2:5, 1:2, ] <- array(1:40, c(4, 2, 5))
> a[2:5, 1:2, ] <- array(1:40, c(4, 2, 5))
> stopifnot(identical(a, as.array(A)))
> 
> ## Other operations:
> crazy <- function(x) (5 * x[ , , 1] ^ 3 + 1L) * log(x[, , 2])
> b <- crazy(a)
> head(b)
           [,1]     [,2]        [,3]       [,4]        [,5]        [,6]
[1,]         NA       NA -0.01084111 -0.7911197 -0.81641070 -1.16977624
[2,]  13.183347 1605.658          NA         NA          NA          NA
[3,]  94.405989 2852.821          NA -0.8794406 -0.85620417 -0.03046359
[4,] 326.113757 4647.014          NA         NA -0.02579455          NA
[5,] 797.655035 7100.600          NA -0.6519162 -0.23365954 -0.90290089
[6,]  -3.712444       NA          NA -2.0995609 -0.83321177          NA
            [,7]        [,8]       [,9]      [,10]      [,11]      [,12]
[1,] -0.67772499 -1.66983724 -0.1203020 -3.0180748 -2.4149643 -0.9858752
[2,] -0.08532778          NA         NA -0.3462271         NA -1.0420006
[3,] -0.95921678          NA -0.7947090 -4.9364035 -1.7957957         NA
[4,]          NA          NA -3.6889523         NA -1.3388774         NA
[5,] -1.66917959 -0.02157539         NA         NA -0.5882418 -0.2122509
[6,] -1.45539867 -1.80947488 -0.9231028         NA -3.1099076 -1.3797082
           [,13]      [,14]      [,15]      [,16]      [,17]      [,18]
[1,] -1.44664539         NA         NA -3.4317223         NA         NA
[2,] -0.94193419         NA -0.8839567 -1.9314895 -2.9217679         NA
[3,] -3.64703324 -0.4226855 -0.8910730 -3.0527102 -0.3683111 -0.5079027
[4,] -0.92950178 -1.2200963         NA -2.1433379 -1.6114017         NA
[5,] -0.45836167 -0.9219286 -0.1794420         NA -6.4882565         NA
[6,] -0.07183526         NA -0.9584520 -0.9982236         NA -5.0652569
          [,19]       [,20]      [,21]      [,22]      [,23]      [,24]
[1,] -0.7415210 -5.40256386 -1.7758007 -1.8927894         NA         NA
[2,] -0.4052647          NA -0.3188749 -0.4159834         NA         NA
[3,] -1.8042459 -0.06911672 -2.5636709 -1.7512667 -3.8590887         NA
[4,]         NA -0.59480388 -5.0345433         NA         NA         NA
[5,] -1.4030591 -0.66094322 -0.7927446         NA -0.3759807 -1.1378558
[6,] -0.2386684 -1.96635486 -5.1529723 -0.5016655 -0.4504479 -0.8596094
          [,25]      [,26]      [,27]     [,28]      [,29]       [,30]
[1,] -1.1890910 -0.7782672         NA        NA         NA          NA
[2,] -0.8530179         NA -1.4104882 -1.359871 -0.7323333 -0.89220745
[3,]         NA -0.3563664         NA -1.096636 -0.6474434 -0.25920369
[4,] -1.1961239         NA -1.7055368 -7.527642 -3.3656538 -0.47473174
[5,] -1.8363278         NA         NA        NA -0.4110371 -0.37141299
[6,] -0.7927169 -1.9311802 -0.5106923        NA         NA -0.07139043
> 
> B <- crazy(A)  # very fast! (all operations are delayed)
> B
<10000 x 30> DelayedMatrix object of type "double":
                  [,1]          [,2]          [,3] ...      [,29]      [,30]
    [1,]            NA            NA   -0.01084111   .         NA         NA
    [2,]   13.18334746 1605.65829777            NA   . -0.7323333 -0.8922074
    [3,]   94.40598881 2852.82097331            NA   . -0.6474434 -0.2592037
    [4,]  326.11375710 4647.01414509            NA   . -3.3656538 -0.4747317
    [5,]  797.65503458 7100.59971766            NA   . -0.4110371 -0.3714130
     ...             .             .             .   .          .          .
 [9996,]    -4.7158859    -5.5416762    -0.4274536   .         NA  -1.560542
 [9997,]            NA    -0.4166767    -0.8340548   .         NA         NA
 [9998,]    -1.0999648    -0.3083348            NA   .  -2.462926         NA
 [9999,]    -0.9052873    -0.6422780            NA   .  -1.026958  -1.129680
[10000,]    -2.0987848            NA    -0.9341993   .         NA  -1.688237
> 
> cs <- colSums(b)
> CS <- colSums(B)
> stopifnot(identical(cs, CS))
> 
> ## ---------------------------------------------------------------------
> ## B. WRAP A DataFrame OBJECT IN A DelayedArray OBJECT
> ## ---------------------------------------------------------------------
> ## Generate random coverage and score along an imaginary chromosome:
> cov <- Rle(sample(20, 5000, replace=TRUE), sample(6, 5000, replace=TRUE))
> score <- Rle(sample(100, nrun(cov), replace=TRUE), runLength(cov))
> 
> DF <- DataFrame(cov, score)
> A2 <- DelayedArray(DF)
> A2
<17491 x 2> DelayedMatrix object of type "integer":
         cov score
    [1,]  20    39
    [2,]  20    39
    [3,]  20    39
    [4,]  20    39
    [5,]   5    94
     ...   .     .
[17487,]  15     4
[17488,]  15     4
[17489,]  17    36
[17490,]  17    36
[17491,]  17    36
> seed(A2)  # 'DF'
DataFrame with 17491 rows and 2 columns
        cov score
      <Rle> <Rle>
1        20    39
2        20    39
3        20    39
4        20    39
5         5    94
...     ...   ...
17487    15     4
17488    15     4
17489    17    36
17490    17    36
17491    17    36
> 
> ## Coercion of a DelayedMatrix object to DataFrame produces a DataFrame
> ## object with Rle columns:
> as(A2, "DataFrame")
DataFrame with 17491 rows and 2 columns
        cov score
      <Rle> <Rle>
1        20    39
2        20    39
3        20    39
4        20    39
5         5    94
...     ...   ...
17487    15     4
17488    15     4
17489    17    36
17490    17    36
17491    17    36
> stopifnot(identical(DF, as(A2, "DataFrame")))
> 
> t(A2)  # transposition is delayed so is very fast and memory-efficient
<2 x 17491> DelayedMatrix object of type "integer":
          [,1]     [,2]     [,3]     [,4] ... [,17488] [,17489] [,17490]
cov         20       20       20       20   .       15       17       17
score       39       39       39       39   .        4       36       36
      [,17491]
cov         17
score       36
> colSums(A2)
   cov  score 
184431 887720 
> 
> ## ---------------------------------------------------------------------
> ## C. AN HDF5Array OBJECT IS A (PARTICULAR KIND OF) DelayedArray OBJECT
> ## ---------------------------------------------------------------------
> library(HDF5Array)
Loading required package: h5mread
Loading required package: rhdf5

Attaching package: ‘h5mread’

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

    h5ls

> A3 <- as(a, "HDF5Array")   # write 'a' to an HDF5 file
> A3
<10000 x 30 x 5> HDF5Array object of type "double":
,,1
              [,1]      [,2]      [,3] ...     [,29]     [,30]
    [1,] 0.2655087        NA 0.2106027   . 0.5984631 0.3642249
    [2,] 1.0000000 5.0000000        NA   . 0.3827384 0.3018117
     ...         .         .         .   .         .         .
 [9999,] 0.5681162 0.6015600        NA   . 0.4622780 0.5157081
[10000,] 0.6526770        NA 0.3413588   .        NA 0.3565323

...

,,5
               [,1]       [,2]       [,3] ...     [,29]     [,30]
    [1,]  0.5412941         NA  0.4245202   . 0.8594370 0.9868373
    [2,] 33.0000000 37.0000000  0.2619832   .        NA 0.3127530
     ...          .          .          .   .         .         .
 [9999,]  0.4552756  0.3828210         NA   . 0.7054346 0.2747098
[10000,]  0.4735345  0.7219708  0.5787122   . 0.7802741 0.8555813

> is(A3, "DelayedArray")     # TRUE
[1] TRUE
> seed(A3)                   # an HDF5ArraySeed object
An object of class "HDF5ArraySeed"
Slot "filepath":
[1] "/tmp/RtmprQSEND/HDF5Array_dump/auto47c06390079c0.h5"

Slot "name":
[1] "/HDF5ArrayAUTO00002"

Slot "as_sparse":
[1] FALSE

Slot "type":
[1] NA

Slot "dim":
[1] 10000    30     5

Slot "chunkdim":
[1] 8735   26    4

Slot "first_val":
[1] 0.2655087

> 
> B3 <- crazy(A3)            # very fast! (all operations are delayed)
> B3                         # not an HDF5Array object anymore because
<10000 x 30> DelayedMatrix object of type "double":
                  [,1]          [,2]          [,3] ...      [,29]      [,30]
    [1,]            NA            NA   -0.01084111   .         NA         NA
    [2,]   13.18334746 1605.65829777            NA   . -0.7323333 -0.8922074
    [3,]   94.40598881 2852.82097331            NA   . -0.6474434 -0.2592037
    [4,]  326.11375710 4647.01414509            NA   . -3.3656538 -0.4747317
    [5,]  797.65503458 7100.59971766            NA   . -0.4110371 -0.3714130
     ...             .             .             .   .          .          .
 [9996,]    -4.7158859    -5.5416762    -0.4274536   .         NA  -1.560542
 [9997,]            NA    -0.4166767    -0.8340548   .         NA         NA
 [9998,]    -1.0999648    -0.3083348            NA   .  -2.462926         NA
 [9999,]    -0.9052873    -0.6422780            NA   .  -1.026958  -1.129680
[10000,]    -2.0987848            NA    -0.9341993   .         NA  -1.688237
>                            # now it carries delayed operations
> CS3 <- colSums(B3)
> stopifnot(identical(cs, CS3))
> 
> ## ---------------------------------------------------------------------
> ## D. PERFORM THE DELAYED OPERATIONS
> ## ---------------------------------------------------------------------
> as(B3, "HDF5Array")        # "realize" 'B3' on disk
<10000 x 30> HDF5Matrix object of type "double":
                  [,1]          [,2]          [,3] ...      [,29]      [,30]
    [1,]            NA            NA   -0.01084111   .         NA         NA
    [2,]   13.18334746 1605.65829777            NA   . -0.7323333 -0.8922074
    [3,]   94.40598881 2852.82097331            NA   . -0.6474434 -0.2592037
    [4,]  326.11375710 4647.01414509            NA   . -3.3656538 -0.4747317
    [5,]  797.65503458 7100.59971766            NA   . -0.4110371 -0.3714130
     ...             .             .             .   .          .          .
 [9996,]    -4.7158859    -5.5416762    -0.4274536   .         NA  -1.560542
 [9997,]            NA    -0.4166767    -0.8340548   .         NA         NA
 [9998,]    -1.0999648    -0.3083348            NA   .  -2.462926         NA
 [9999,]    -0.9052873    -0.6422780            NA   .  -1.026958  -1.129680
[10000,]    -2.0987848            NA    -0.9341993   .         NA  -1.688237
> 
> ## If this is just an intermediate result, you can either keep going
> ## with B3 or replace it with its "realized" version:
> B3 <- as(B3, "HDF5Array")  # no more delayed operations on new 'B3'
> seed(B3)
An object of class "HDF5ArraySeed"
Slot "filepath":
[1] "/tmp/RtmprQSEND/HDF5Array_dump/auto47c061e57b43a.h5"

Slot "name":
[1] "/HDF5ArrayAUTO00004"

Slot "as_sparse":
[1] FALSE

Slot "type":
[1] NA

Slot "dim":
[1] 10000    30

Slot "chunkdim":
[1] 10000    30

Slot "first_val":
[1] NA

> path(B3)
[1] "/tmp/RtmprQSEND/HDF5Array_dump/auto47c061e57b43a.h5"
> 
> ## For convenience, realize() can be used instead of explicit coercion.
> ## The current "automatic realization backend" controls where
> ## realization happens e.g. in memory if set to NULL or in an HDF5
> ## file if set to "HDF5Array":
> D <- cbind(B3, exp(B3))
> D
<10000 x 60> DelayedMatrix object of type "double":
                  [,1]          [,2]          [,3] ...      [,59]      [,60]
    [1,]            NA            NA   -0.01084111   .         NA         NA
    [2,]   13.18334746 1605.65829777            NA   . 0.48078587 0.40975025
    [3,]   94.40598881 2852.82097331            NA   . 0.52338217 0.77166582
    [4,]  326.11375710 4647.01414509            NA   . 0.03453943 0.62205191
    [5,]  797.65503458 7100.59971766            NA   . 0.66296233 0.68975902
     ...             .             .             .   .          .          .
 [9996,]    -4.7158859    -5.5416762    -0.4274536   .         NA 0.21002231
 [9997,]            NA    -0.4166767    -0.8340548   .         NA         NA
 [9998,]    -1.0999648    -0.3083348            NA   . 0.08518537         NA
 [9999,]    -0.9052873    -0.6422780            NA   . 0.35809468 0.32313660
[10000,]    -2.0987848            NA    -0.9341993   .         NA 0.18484508
> setAutoRealizationBackend("HDF5Array")
> D <- realize(D)
Error in H5Dwrite(h5dataset, obj, h5spaceMem = h5spaceMem, h5spaceFile = h5spaceFile) : 
  HDF5. Dataset. Write failed.
Error in H5Fclose(file$H5Identifier) : 
  HDF5. Object cache. Internal error detected.
Calls: realize ... h5write -> h5write.default -> h5closeitLoc -> H5Fclose
Execution halted

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 ERROR
Running the tests in ‘tests/run_unitTests.R’ failed.
Last 13 lines of output:
  DelayedArray RUnit Tests - 43 test functions, 1 error, 0 failures
  ERROR in test_BLOCK_mult_Lgrid_Rgrid: Error in H5Fcreate(file) : HDF5. File accessibility. Unable to open file.
  
  Test files with failing tests
  
     test_DelayedMatrix-mult.R 
       test_BLOCK_mult_Lgrid_Rgrid 
  
  
  Error in BiocGenerics:::testPackage("DelayedArray") : 
    unit tests failed for package DelayedArray
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
  HDF5: infinite loop closing library
        L,T_top,P,P,Z,FD,PL,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL
* 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, 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

Timing stopped at: 3.468 0.036 3.137
Error in H5Fcreate(file) : HDF5. File accessibility. Unable to open file.
In addition: Warning messages:
1: In log(a + 0.2) : NaNs produced
2: In OP(a) : NaNs produced

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.
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 -- Fri Apr  4 19:58:27 2025 
*********************************************** 
Number of test functions: 43 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
DelayedArray RUnit Tests - 43 test functions, 1 error, 0 failures
ERROR in test_BLOCK_mult_Lgrid_Rgrid: Error in H5Fcreate(file) : HDF5. File accessibility. Unable to open file.

Test files with failing tests

   test_DelayedMatrix-mult.R 
     test_BLOCK_mult_Lgrid_Rgrid 


Error in BiocGenerics:::testPackage("DelayedArray") : 
  unit tests failed for package DelayedArray
Calls: <Anonymous> -> <Anonymous>
Execution halted
HDF5: infinite loop closing library
      L,T_top,P,P,Z,FD,PL,E,SL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL,FL