##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HDF5Array_1.39.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/HDF5Array.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-21 05:26:34 UTC
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.39.1’
* 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 ... 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 ‘HDF5Array’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
* 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:
  H5SparseMatrix-class.Rd: h5ls
  H5SparseMatrixSeed-class.Rd: h5ls
  HDF5Array-class.Rd: H5File, h5ls
  HDF5ArraySeed-class.Rd: h5ls
  ReshapedHDF5Array-class.Rd: h5ls
  ReshapedHDF5ArraySeed-class.Rd: h5ls
  TENxMatrix-class.Rd: h5ls
  TENxMatrixSeed-class.Rd: h5ls
  dump-management.Rd: h5createDataset, h5ls
  writeHDF5Array.Rd: DelayedArray, h5writeDimnames, h5ls
  writeTENxMatrix.Rd: DelayedMatrix, h5ls
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘HDF5Array-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDF5Array-class
> ### Title: HDF5 datasets as DelayedArray objects
> ### Aliases: class:HDF5Array HDF5Array-class HDF5Array
> ###   DelayedArray,HDF5ArraySeed-method class:HDF5Matrix HDF5Matrix-class
> ###   HDF5Matrix is_sparse<-,HDF5Array-method matrixClass,HDF5Array-method
> ###   coerce,HDF5Array,HDF5Matrix-method coerce,HDF5Matrix,HDF5Array-method
> ###   coerce,ANY,HDF5Matrix-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. CONSTRUCTION
> ## ---------------------------------------------------------------------
> 
> ## With a local file:
> toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array")
> h5ls(toy_h5)
  group name       otype dclass         dim
0     /   M1 H5I_DATASET  FLOAT 10000 x 150
1     /   M2 H5I_DATASET  FLOAT   150 x 200
> 
> HDF5Array(toy_h5, "M2")
<150 x 200> HDF5Matrix object of type "double":
             [,1]       [,2]       [,3] ...       [,199]       [,200]
  [1,]  9.0325451 -0.8372894 -3.0655634   .     4.202503     7.212745
  [2,]  0.5603696  1.4590217  1.6268596   .    14.854123     3.481012
  [3,]  8.1094489  2.9110584 12.7574103   .     0.520843     8.876323
  [4,]  5.8518510  6.4912588 13.8403073   .     8.795605    12.342113
  [5,] -0.8206218 10.1040618 10.6219819   .     8.756145     3.130079
   ...          .          .          .   .            .            .
[146,] 11.2827878 -3.7808660  5.4538427   . -0.762771429  6.070777178
[147,] -2.3159837 10.5172435 -2.9781124   .  0.824398901 -3.154179584
[148,]  0.9635204 13.8644578 11.6860867   .  5.761504602  1.688992344
[149,] 12.6951503 11.6835890 13.4213585   . 13.590451800  2.134752800
[150,] -1.8871983  9.9152485  8.6534266   . -0.007439521  7.164514768
> HDF5Array(toy_h5, "M2", type="integer")
<150 x 200> HDF5Matrix object of type "integer":
         [,1]   [,2]   [,3]   [,4] ... [,197] [,198] [,199] [,200]
  [1,]      9      0     -3     14   .     -1     11      4      7
  [2,]      0      1      1     14   .     12      6     14      3
  [3,]      8      2     12      6   .     10      0      0      8
  [4,]      5      6     13     12   .     -1      6      8     12
  [5,]      0     10     10     -4   .      9     14      8      3
   ...      .      .      .      .   .      .      .      .      .
[146,]     11     -3      5      0   .      1      6      0      6
[147,]     -2     10     -2     -1   .      3      9      0     -3
[148,]      0     13     11     -2   .      2     -4      5      1
[149,]     12     11     13      8   .     13      3     13      2
[150,]     -1      9      8      9   .     10     -2      0      7
> HDF5Array(toy_h5, "M2", type="complex")
<150 x 200> HDF5Matrix object of type "complex":
                [,1]          [,2]          [,3] ...          [,199]
  [1,]  9.0325451+0i -0.8372894+0i -3.0655634+0i   .     4.202503+0i
  [2,]  0.5603696+0i  1.4590217+0i  1.6268596+0i   .    14.854123+0i
  [3,]  8.1094489+0i  2.9110584+0i 12.7574103+0i   .     0.520843+0i
  [4,]  5.8518510+0i  6.4912588+0i 13.8403073+0i   .     8.795605+0i
  [5,] -0.8206218+0i 10.1040618+0i 10.6219819+0i   .     8.756145+0i
   ...             .             .             .   .               .
[146,] 11.2827878+0i -3.7808660+0i  5.4538427+0i   . -0.762771429+0i
[147,] -2.3159837+0i 10.5172435+0i -2.9781124+0i   .  0.824398901+0i
[148,]  0.9635204+0i 13.8644578+0i 11.6860867+0i   .  5.761504602+0i
[149,] 12.6951503+0i 11.6835890+0i 13.4213585+0i   . 13.590451800+0i
[150,] -1.8871983+0i  9.9152485+0i  8.6534266+0i   . -0.007439521+0i
                [,200]
  [1,]     7.212745+0i
  [2,]     3.481012+0i
  [3,]     8.876323+0i
  [4,]    12.342113+0i
  [5,]     3.130079+0i
   ...               .
[146,]  6.070777178+0i
[147,] -3.154179584+0i
[148,]  1.688992344+0i
[149,]  2.134752800+0i
[150,]  7.164514768+0i
> 
> ## With a file stored in an Amazon S3 bucket:
> if (Sys.info()[["sysname"]] != "Darwin") {
+     public_S3_url <-
+      "https://rhdf5-public.s3.eu-central-1.amazonaws.com/rhdf5ex_t_float_3d.h5"
+     h5file <- H5File(public_S3_url, s3=TRUE)
+     h5ls(h5file)
+ 
+     HDF5Array(h5file, "a1")
+ }
<5 x 10 x 2> HDF5Array object of type "double":
,,1
            [,1]        [,2]        [,3] ...       [,9]      [,10]
[1,] 0.122377600 0.473829743 0.244448476   . 0.06294312 0.25262216
[2,] 0.257908699 0.009508783 0.387372283   . 0.52225184 0.94390880
[3,] 0.886223679 0.211665150 0.404533111   . 0.95703000 0.18594012
[4,] 0.549336179 0.071420332 0.617852765   . 0.20320586 0.48317974
[5,] 0.179772913 0.557769188 0.553050760   . 0.72190719 0.18467657

,,2
          [,1]      [,2]      [,3] ...       [,9]      [,10]
[1,] 0.6848327 0.1282442 0.7906603   . 0.40603368 0.01085798
[2,] 0.6579706 0.4897645 0.3274960   . 0.47773518 0.38283946
[3,] 0.7180033 0.4929566 0.2159982   . 0.48220542 0.56122233
[4,] 0.8445332 0.8016226 0.8083879   . 0.26790274 0.17247477
[5,] 0.4086140 0.3476558 0.7067179   . 0.18221174 0.99788310

> 
> ## ---------------------------------------------------------------------
> ## B. BASIC MANIPULATION
> ## ---------------------------------------------------------------------
> 
> library(h5vcData)
> tally_file <- system.file("extdata", "example.tally.hfs5",
+                           package="h5vcData")
> h5ls(tally_file)
              group         name       otype  dclass                   dim
0                 / ExampleStudy   H5I_GROUP                              
1     /ExampleStudy           16   H5I_GROUP                              
2  /ExampleStudy/16       Counts H5I_DATASET INTEGER 12 x 6 x 2 x 90354753
3  /ExampleStudy/16    Coverages H5I_DATASET INTEGER      6 x 2 x 90354753
4  /ExampleStudy/16    Deletions H5I_DATASET INTEGER      6 x 2 x 90354753
5  /ExampleStudy/16    Reference H5I_DATASET INTEGER              90354753
6     /ExampleStudy           22   H5I_GROUP                              
7  /ExampleStudy/22       Counts H5I_DATASET INTEGER 12 x 6 x 2 x 51304566
8  /ExampleStudy/22    Coverages H5I_DATASET INTEGER      6 x 2 x 51304566
9  /ExampleStudy/22    Deletions H5I_DATASET INTEGER      6 x 2 x 51304566
10 /ExampleStudy/22    Reference H5I_DATASET INTEGER              51304566
> 
> ## Pick up "Coverages" dataset for Human chromosome 16:
> name <- "/ExampleStudy/16/Coverages"
> cvg <- HDF5Array(tally_file, name)
> cvg
<6 x 2 x 90354753> HDF5Array object of type "integer":
,,1
     [,1] [,2]
[1,]    0    0
[2,]    0    0
 ...    .    .
[5,]    0    0
[6,]    0    0

...

,,90354753
     [,1] [,2]
[1,]    0    0
[2,]    0    0
 ...    .    .
[5,]    0    0
[6,]    0    0

> 
> is(cvg, "DelayedArray")  # TRUE
[1] TRUE
> seed(cvg)
An object of class "HDF5ArraySeed"
Slot "filepath":
[1] "/home/biocbuild/bbs-3.23-bioc/R/site-library/h5vcData/extdata/example.tally.hfs5"

Slot "name":
[1] "/ExampleStudy/16/Coverages"

Slot "as_sparse":
[1] FALSE

Slot "type":
[1] NA

Slot "dim":
[1]        6        2 90354753

Slot "chunkdim":
[1]     1     1 88238

Slot "first_val":
[1] 0

> path(cvg)
[1] "/home/biocbuild/bbs-3.23-bioc/R/site-library/h5vcData/extdata/example.tally.hfs5"
> chunkdim(cvg)
[1]     1     1 88238
> 
> ## The data in the dataset looks sparse. In this case it is recommended
> ## to set 'as.sparse' to TRUE when constructing the HDF5Array object.
> ## This will make block processing (used in operations like sum()) more
> ## memory efficient and likely faster:
> cvg0 <- HDF5Array(tally_file, name, as.sparse=TRUE)
> is_sparse(cvg0)  # TRUE
[1] TRUE
> 
> ## Note that we can also flag the HDF5Array object as sparse after
> ## creation:
> is_sparse(cvg) <- TRUE
> cvg  # same as 'cvg0'
<6 x 2 x 90354753> sparse HDF5Array object of type "integer":
,,1
     [,1] [,2]
[1,]    0    0
[2,]    0    0
 ...    .    .
[5,]    0    0
[6,]    0    0

...

Error in .Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE = "h5mread") : 
  failed to open HDF5 file '/home/biocbuild/bbs-3.23-bioc/R/site-library/h5vcData/extdata/example.tally.hfs5'
Calls: <Anonymous> ... h5readDimnames -> get_h5dimnames -> h5getdimscales -> .Call2
Execution halted
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL HDF5Array
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘HDF5Array’ ...
** this is package ‘HDF5Array’ version ‘1.39.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HDF5Array)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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.

> require("HDF5Array") || stop("unable to load HDF5Array package")
Loading required package: HDF5Array
Loading required package: SparseArray
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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, unname

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

    findMatches

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

    I, expand.grid, unname

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

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

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

[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    rowMedians

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

    anyMissing, rowMedians

For native R and reading and writing of H5AD files, an R <AnnData> object, and
conversion to <SingleCellExperiment> or <Seurat> objects, check out the
anndataR package:
ℹ Install it from Bioconductor with `BiocManager::install("anndataR")`
ℹ See more at <https://bioconductor.org/packages/anndataR/>
This message is displayed once per session.
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)
automatic block size set to 77 bytes (was 1e+08)
automatic block size set to 1e+08 bytes (was 77)


RUNIT TEST PROTOCOL -- Tue Apr 21 01:29:05 2026 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 14.079   0.804  21.195