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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HDF5Array_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.34.0’
* 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
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... NOTE
  installed size is 22.6Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     13.9Mb
* checking package 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 ... NOTE
Unexported object imported by a ':::' call: ‘rhdf5:::h5checktypeOrOpenLocS3’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.4.2/site-library/HDF5Array/libs/HDF5Array.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘printf’, possibly from ‘printf’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... ERROR
Running examples in ‘HDF5Array-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TENxMatrix-class
> ### Title: 10x Genomics datasets as DelayedMatrix objects
> ### Aliases: class:TENxMatrix TENxMatrix-class TENxMatrix
> ###   DelayedArray,TENxMatrixSeed-method nzcount,TENxMatrix-method
> ###   read_sparse_block,TENxMatrix-method
> ###   extractNonzeroDataByCol,TENxMatrix-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## SIMPLE TENxMatrix EXAMPLE
> ## ---------------------------------------------------------------------
> 
> sm <- Matrix::rsparsematrix(10, 7, density=0.3)
> M <- writeTENxMatrix(sm)
> M
<10 x 7> sparse TENxMatrix object of type "double":
        [,1]   [,2]   [,3] ...   [,6]   [,7]
 [1,]  1.100  0.000  0.075   .  0.920  0.000
 [2,]  0.000  0.000  0.000   .  0.000  0.000
 [3,]  0.000  0.000  0.000   .  0.000 -0.100
 [4,]  0.000  0.940  0.000   . -0.056  0.000
 [5,]  0.000  1.400  0.000   .  0.000  0.000
 [6,]  0.000  0.000  0.000   .  0.000  0.000
 [7,] -0.480  0.000  0.000   .  0.000  0.000
 [8,]  0.000  0.820  0.000   .  0.000 -0.620
 [9,]  0.420  0.000  0.000   .  0.590  0.000
[10,] -1.500  0.000  0.000   . -2.000  0.000
> 
> class(M)  # TENxMatrix
[1] "TENxMatrix"
attr(,"package")
[1] "HDF5Array"
> is(M, "DelayedMatrix")  # TRUE
[1] TRUE
> 
> seed(M)
<10 x 7> sparse TENxMatrixSeed object of type "double":
# dirname: /home/biocbuild/tmp/RtmpAJMvps/HDF5Array_dump
# basename: auto3abc9652b9a994.h5
# group: /HDF5ArrayAUTO00001
> class(seed(M))  # TENxMatrixSeed
[1] "TENxMatrixSeed"
attr(,"package")
[1] "HDF5Array"
> 
> rhdf5::h5ls(path(M))
                group               name       otype  dclass dim
0                   / HDF5ArrayAUTO00001   H5I_GROUP            
1 /HDF5ArrayAUTO00001               data H5I_DATASET   FLOAT  21
2 /HDF5ArrayAUTO00001            indices H5I_DATASET INTEGER  21
3 /HDF5ArrayAUTO00001             indptr H5I_DATASET INTEGER   8
4 /HDF5ArrayAUTO00001              shape H5I_DATASET INTEGER   2
> 
> is_sparse(M)  # TRUE
[1] TRUE
> 
> ## Use coercion to load the full dataset into memory:
> as.matrix(M)          # as ordinary array (usually not recommended)
       [,1] [,2]  [,3]   [,4]   [,5]   [,6]  [,7]
 [1,]  1.10 0.00 0.075  0.000  0.000  0.920  0.00
 [2,]  0.00 0.00 0.000  0.000  0.620  0.000  0.00
 [3,]  0.00 0.00 0.000  0.780 -0.016  0.000 -0.10
 [4,]  0.00 0.94 0.000 -0.045  0.000 -0.056  0.00
 [5,]  0.00 1.40 0.000  0.000  0.000  0.000  0.00
 [6,]  0.00 0.00 0.000  0.000 -0.160  0.000  0.00
 [7,] -0.48 0.00 0.000  0.390  0.000  0.000  0.00
 [8,]  0.00 0.82 0.000  0.000  0.000  0.000 -0.62
 [9,]  0.42 0.00 0.000 -2.200  0.000  0.590  0.00
[10,] -1.50 0.00 0.000  0.000  0.000 -2.000  0.00
> as(M, "dgCMatrix")    # as dgCMatrix (brings back 'sm')
10 x 7 sparse Matrix of class "dgCMatrix"
                                                 
 [1,]  1.10 .    0.075  .      .      0.920  .   
 [2,]  .    .    .      .      0.620  .      .   
 [3,]  .    .    .      0.780 -0.016  .     -0.10
 [4,]  .    0.94 .     -0.045  .     -0.056  .   
 [5,]  .    1.40 .      .      .      .      .   
 [6,]  .    .    .      .     -0.160  .      .   
 [7,] -0.48 .    .      0.390  .      .      .   
 [8,]  .    0.82 .      .      .      .     -0.62
 [9,]  0.42 .    .     -2.200  .      0.590  .   
[10,] -1.50 .    .      .      .     -2.000  .   
> as(M, "SparseArray")  # as SparseArray object (most efficient)
<10 x 7 SparseMatrix> of type "double" [nzcount=21 (30%)]:
        [,1]   [,2]   [,3] ...   [,6]   [,7]
 [1,]  1.100  0.000  0.075   .  0.920  0.000
 [2,]  0.000  0.000  0.000   .  0.000  0.000
 [3,]  0.000  0.000  0.000   .  0.000 -0.100
 [4,]  0.000  0.940  0.000   . -0.056  0.000
 [5,]  0.000  1.400  0.000   .  0.000  0.000
 [6,]  0.000  0.000  0.000   .  0.000  0.000
 [7,] -0.480  0.000  0.000   .  0.000  0.000
 [8,]  0.000  0.820  0.000   .  0.000 -0.620
 [9,]  0.420  0.000  0.000   .  0.590  0.000
[10,] -1.500  0.000  0.000   . -2.000  0.000
> SparseArray(M)        # equivalent to 'as(M, "SparseArray")'
<10 x 7 SparseMatrix> of type "double" [nzcount=21 (30%)]:
        [,1]   [,2]   [,3] ...   [,6]   [,7]
 [1,]  1.100  0.000  0.075   .  0.920  0.000
 [2,]  0.000  0.000  0.000   .  0.000  0.000
 [3,]  0.000  0.000  0.000   .  0.000 -0.100
 [4,]  0.000  0.940  0.000   . -0.056  0.000
 [5,]  0.000  1.400  0.000   .  0.000  0.000
 [6,]  0.000  0.000  0.000   .  0.000  0.000
 [7,] -0.480  0.000  0.000   .  0.000  0.000
 [8,]  0.000  0.820  0.000   .  0.000 -0.620
 [9,]  0.420  0.000  0.000   .  0.590  0.000
[10,] -1.500  0.000  0.000   . -2.000  0.000
> 
> ## ---------------------------------------------------------------------
> ## THE "1.3 Million Brain Cell Dataset" AS A DelayedMatrix OBJECT
> ## ---------------------------------------------------------------------
> 
> ## The 1.3 Million Brain Cell Dataset from 10x Genomics is available
> ## via ExperimentHub:
> 
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> hub <- ExperimentHub()
> query(hub, "TENxBrainData")
ExperimentHub with 8 records
# snapshotDate(): 2024-10-24
# $dataprovider: 10X Genomics
# $species: Mus musculus
# $rdataclass: character
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["EH1039"]]' 

           title                                                            
  EH1039 | Brain scRNA-seq data, 'HDF5-based 10X Genomics' format           
  EH1040 | Brain scRNA-seq data, 'dense matrix' format                      
  EH1041 | Brain scRNA-seq data, sample (column) annotation                 
  EH1042 | Brain scRNA-seq data, gene (row) annotation                      
  EH1689 | Brain scRNA-seq data 20k subset, 'HDF5-based 10x Genomics' format
  EH1690 | Brain scRNA-seq data 20k subset, 'dense matrix' format           
  EH1691 | Brain scRNA-seq data 20k subset, sample (column) annotation      
  EH1692 | Brain scRNA-seq data 20k subset, gene (row) annotation           
> fname <- hub[["EH1039"]]
see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
loading from cache
> 
> ## 'fname' is an HDF5 file. Use h5ls() to list its content:
> h5ls(fname)
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) : 
  HDF5. File accessibility. Unable to open file.
Calls: h5ls -> <Anonymous> -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.