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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:HDF5Array.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings HDF5Array_1.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/HDF5Array.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* this is package ‘HDF5Array’ version ‘1.32.0’
* 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: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is 26.3Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
    libs     17.6Mb
* 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-beta-2024-04-15_r86425/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: h5mread
> ### Title: An alternative to 'rhdf5::h5read'
> ### Aliases: get_h5mread_returned_type h5mread
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## BASIC USAGE
> ## ---------------------------------------------------------------------
> m0 <- matrix((runif(600) - 0.5) * 10, ncol=12)
> M0 <- writeHDF5Array(m0, name="M0")
> 
> m <- h5mread(path(M0), "M0")
> stopifnot(identical(m0, m))
> 
> m <- h5mread(path(M0), "M0", starts=list(NULL, c(3, 12:8)))
> stopifnot(identical(m0[ , c(3, 12:8)], m))
> 
> m <- h5mread(path(M0), "M0", starts=list(integer(0), c(3, 12:8)))
> stopifnot(identical(m0[NULL , c(3, 12:8)], m))
> 
> m <- h5mread(path(M0), "M0", starts=list(1:5, NULL), as.integer=TRUE)
> storage.mode(m0) <- "integer"
> stopifnot(identical(m0[1:5, ], m))
> 
> a0 <- array(1:350, c(10, 5, 7))
> A0 <- writeHDF5Array(a0, filepath=path(M0), name="A0")
> h5ls(path(A0))
  group name       otype  dclass        dim
0     /   A0 H5I_DATASET INTEGER 10 x 5 x 7
1     /   M0 H5I_DATASET   FLOAT    50 x 12
> 
> a <- h5mread(path(A0), "A0", starts=list(c(2, 7), NULL, 6),
+                              counts=list(c(4, 2), NULL, NULL))
> stopifnot(identical(a0[c(2:5, 7:8), , 6, drop=FALSE], a))
> 
> ## Load the data in a sparse array representation:
> 
> m1 <- matrix(c(5:-2, rep.int(c(0L, 99L), 11)), ncol=6)
> M1 <- writeHDF5Array(m1, name="M1", chunkdim=c(3L, 2L))
> 
> index <- list(5:3, NULL)
> m <- h5mread(path(M1), "M1", starts=index)
> sas <- h5mread(path(M1), "M1", starts=index, as.sparse=TRUE)
> class(sas)  # SparseArraySeed object (see ?SparseArraySeed)
[1] "SparseArraySeed"
attr(,"package")
[1] "DelayedArray"
> as(sas, "dgCMatrix")
3 x 6 sparse Matrix of class "dgCMatrix"
                     
[1,] 1 99  . 99  . 99
[2,] 2  . 99  . 99  .
[3,] 3 -2  . 99  . 99
> stopifnot(identical(m, sparse2dense(sas)))
> 
> ## ---------------------------------------------------------------------
> ## PERFORMANCE
> ## ---------------------------------------------------------------------
> library(ExperimentHub)
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
> hub <- ExperimentHub()
> 
> ## With the "sparse" TENxBrainData dataset
> ## ---------------------------------------
> fname0 <- hub[["EH1039"]]
see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
loading from cache
> h5ls(fname0)  # all datasets are 1D datasets
  group       name       otype  dclass        dim
0     /       mm10   H5I_GROUP                   
1 /mm10   barcodes H5I_DATASET  STRING    1306127
2 /mm10       data H5I_DATASET INTEGER 2624828308
3 /mm10 gene_names H5I_DATASET  STRING      27998
4 /mm10      genes H5I_DATASET  STRING      27998
5 /mm10    indices H5I_DATASET INTEGER 2624828308
6 /mm10     indptr H5I_DATASET INTEGER    1306128
7 /mm10      shape H5I_DATASET INTEGER          2
> 
> index <- list(77 * sample(34088679, 5000, replace=TRUE))
> ## h5mread() is about 4x faster than h5read():
> system.time(a <- h5mread(fname0, "mm10/data", index))
   user  system elapsed 
  1.765   0.206   4.502 
> system.time(b <- h5read(fname0, "mm10/data", index=index))
   user  system elapsed 
 12.455   0.102  12.572 
> stopifnot(identical(a, b))
> 
> index <- list(sample(1306127, 7500, replace=TRUE))
> ## h5mread() is about 20x faster than h5read():
> system.time(a <- h5mread(fname0, "mm10/barcodes", index))
   user  system elapsed 
  0.144   0.008   0.151 
> system.time(b <- h5read(fname0, "mm10/barcodes", index=index))
   user  system elapsed 
  6.592   0.076   6.679 
> stopifnot(identical(a, b))
> 
> ## With the "dense" TENxBrainData dataset
> ## --------------------------------------
> fname1 <- hub[["EH1040"]]
see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
loading from cache
> h5ls(fname1)  # "counts" is a 2D dataset
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-3.19-bioc/meat/HDF5Array.Rcheck/00check.log’
for details.