##############################################################################
##############################################################################
###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL HDF5Array
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c H5File.c -o H5File.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c uaselection.c -o uaselection.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5mread_helpers.c -o h5mread_helpers.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c ChunkIterator.c -o ChunkIterator.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5mread_index.c -o h5mread_index.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: ‘NOT_USED_make_nzindex_from_bufs’ defined but not used [-Wunused-function]
  206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: ‘NOT_USED_make_nzdata_from_IntAE_bufs’ defined but not used [-Wunused-function]
  179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: ‘NOT_USED_make_nzindex_from_buf’ defined but not used [-Wunused-function]
  123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5mread.c -o h5mread.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c h5summarize.c -o h5summarize.o
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (HDF5Array)

R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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: DelayedArray
Loading required package: stats4
Loading required package: Matrix
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

Loading required package: rhdf5

Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

[1] TRUE
> HDF5Array:::.test()
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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

/home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
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 -- Thu May  9 08:21:10 2024 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HDF5Array RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 47.675   2.301  59.521