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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:h5mread.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings h5mread_0.99.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/h5mread.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘h5mread/DESCRIPTION’ ... OK
* this is package ‘h5mread’ version ‘0.99.4’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘h5mread’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is 16.6Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     13.9Mb
* 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 ... 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 ... INFO
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-4.5.0-devel_2024-11-24/site-library/h5mread/libs/h5mread.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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘h5mread-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 EXAMPLES
> ## ---------------------------------------------------------------------
> test_h5 <- system.file("extdata", "test.h5", package="h5mread")
> h5ls(test_h5)
Warning in h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native) :
  An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
          group         name       otype  dclass          dim
0             / .m2_dimnames   H5I_GROUP                     
1 /.m2_dimnames            1 H5I_DATASET  STRING         4000
2 /.m2_dimnames            2 H5I_DATASET  STRING           90
3             /           a3 H5I_DATASET INTEGER 180 x 75 x 4
4             /           m1 H5I_DATASET INTEGER       12 x 5
5             /           m2 H5I_DATASET   FLOAT    4000 x 90
6             /           m4 H5I_DATASET INTEGER    28 x 4000
7             /       rwords H5I_DATASET  STRING        30000
> 
> m1 <- h5mread(test_h5, "m1")  # 12 x 5 integer matrix
> 
> m <- h5mread(test_h5, "m1", starts=list(c(8, 12:7), NULL))
> m
     [,1] [,2] [,3] [,4] [,5]
[1,]  108  120  132  144  156
[2,]  112  124  136  148  160
[3,]  111  123  135  147  159
[4,]  110  122  134  146  158
[5,]  109  121  133  145  157
[6,]  108  120  132  144  156
[7,]  107  119  131  143  155
> 
> ## Sanity check:
> stopifnot(identical(m1[c(8, 12:7), ], m))
> 
> m <- h5mread(test_h5, "m1", starts=list(c(8, 12:7), integer(0)))
> m
    
[1,]
[2,]
[3,]
[4,]
[5,]
[6,]
[7,]
> 
> ## Sanity check:
> stopifnot(identical(m1[c(8, 12:7), NULL], m))
> 
> m2 <- h5mread(test_h5, "m2")  # 4000 x 90 double matrix
> 
> m2a <- h5mread(test_h5, "m2", starts=list(31, 1), counts=list(10, 8))
> m2a
            [,1]       [,2]       [,3]       [,4]       [,5]       [,6]
 [1,]  4.6302423  3.6920781  2.5704878  3.8089040 -0.7006228  2.8039929
 [2,]  4.0229905 -0.6359713  4.1256160 -4.1306267 -0.4303055  2.0140353
 [3,]  1.9070528 -3.7952366 -2.0674090 -2.5155661 -4.6262732 -0.1125200
 [4,]  2.9546742  1.1895336  0.5573193  3.3682705  3.7067432 -4.2372909
 [5,] -4.7538632 -0.1949125 -3.0470539 -1.2498946  4.0524254  1.3917748
 [6,] -0.2220403  4.2389309  2.7640452  0.7412419 -0.4210158  2.5244328
 [7,]  2.5845954 -2.5932731  0.9087094 -2.4473713  2.6756166 -4.0774453
 [8,] -2.8359206  2.7648158  0.4323687 -4.8216287 -2.7992909  3.9625529
 [9,] -1.8181899  2.5198789 -3.2706827 -0.6458960  3.3948262 -2.5945095
[10,] -2.6837421  1.7648242  4.0621661  4.0650954  1.1591354 -0.1142555
            [,7]      [,8]
 [1,] -0.2448190 -3.022135
 [2,] -2.8104900  3.098096
 [3,] -2.2713924 -3.524646
 [4,]  2.9222810 -3.140645
 [5,]  1.0613606  4.821568
 [6,]  2.2018533 -3.013025
 [7,] -3.3362339  1.122616
 [8,]  2.2856397  3.749805
 [9,]  0.7560304  2.855820
[10,] -4.7331954  1.640497
> 
> ## Sanity check:
> stopifnot(identical(m2[31:40, 1:8], m2a))
> 
> m2b <- h5mread(test_h5, "m2", starts=list(31, 1), counts=list(10, 8),
+                as.integer=TRUE)
> m2b
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
 [1,]    4    3    2    3    0    2    0   -3
 [2,]    4    0    4   -4    0    2   -2    3
 [3,]    1   -3   -2   -2   -4    0   -2   -3
 [4,]    2    1    0    3    3   -4    2   -3
 [5,]   -4    0   -3   -1    4    1    1    4
 [6,]    0    4    2    0    0    2    2   -3
 [7,]    2   -2    0   -2    2   -4   -3    1
 [8,]   -2    2    0   -4   -2    3    2    3
 [9,]   -1    2   -3    0    3   -2    0    2
[10,]   -2    1    4    4    1    0   -4    1
> 
> ## Sanity check:
> storage.mode(m2a) <- "integer"
> stopifnot(identical(m2a, m2b))
> 
> a3 <- h5mread(test_h5, "a3")  # 180 x 75 x 4 integer array
> 
> starts <- list(c(21, 101), NULL, 3:4)
> counts <- list(c( 5,  22), NULL, NULL)
> a <- h5mread(test_h5, "a3", starts=starts, counts=counts)
> dim(a)
[1] 27 75  2
> a[1:10, 1:12, ]
, , 1

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
 [1,]    0    0    0    0    0    0    0    1    0     0     0     0
 [2,]    0    1    1    0    1    0    0    0    0     0     1     0
 [3,]    0    0    0    0    1    0    0    2    0     0     0     0
 [4,]    0    0    0    0    0    0    0    0    0     0     2     0
 [5,]    0    0    0    0    0    0    0    0    0     0     0     1
 [6,]    0    0    0    0    0    0    0    0    0     1     0     0
 [7,]    0    0    0    0    0    0    0    0    0     0     0     0
 [8,]    0    0    0    1    0    0    0    0    0     0     1     0
 [9,]    1    0    0    0    0    0    0    0    0     0     0     1
[10,]    0    0    0    1    1    0    0    0    0     0     0     0

, , 2

      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
 [1,]    1    0    0    0    0    0    0    0    1     0     0     0
 [2,]    0    0    0    0    0    0    1    0    0     0     0     0
 [3,]    1    0    1    0    0    0    0    0    1     0     0     1
 [4,]    0    0    0    0    0    0    0    0    0     0     0     0
 [5,]    0    0    0    0    1    0    0    0    0     0     1     0
 [6,]    0    0    0    0    0    0    0    0    0     0     0     0
 [7,]    0    0    0    0    0    0    0    1    0     0     0     0
 [8,]    0    0    0    0    0    1    0    0    0     0     0     1
 [9,]    0    0    0    0    0    0    1    0    0     0     0     0
[10,]    1    0    0    0    0    0    0    1    0     0     0     0

> 
> ## Sanity check:
> stopifnot(identical(a3[c(21:25, 101:122), , 3:4, drop=FALSE], a))
> 
> ## ---------------------------------------------------------------------
> ## RETURNING THE DATA AS A SPARSE ARRAY
> ## ---------------------------------------------------------------------
> 
> starts <- list(c(21:25, 101:122), NULL, 3:4)
> coo <- h5mread(test_h5, "a3", starts=starts, as.sparse=TRUE)
> coo
<27 x 75 x 2 SparseArray> of type "integer" [nzcount=577 (14%)]:
,,1
       [,1]  [,2]  [,3]  [,4] ... [,72] [,73] [,74] [,75]
 [1,]     0     0     0     0   .     0     0     0     0
 [2,]     0     1     1     0   .     0     0     0     0
  ...     .     .     .     .   .     .     .     .     .
[26,]     0     0     0     0   .     0     0     1     0
[27,]     1     0     0     0   .     0     0     0     0

,,2
       [,1]  [,2]  [,3]  [,4] ... [,72] [,73] [,74] [,75]
 [1,]     1     0     0     0   .     0     0     0     0
 [2,]     0     0     0     0   .     0     0     0     0
  ...     .     .     .     .   .     .     .     .     .
[26,]     0     0     0     1   .     0     1     1     0
[27,]     1     0     1     1   .     0     0     0     0

> 
> class(coo)  # COO_SparseArray object (see ?COO_SparseArray)
[1] "COO_SparseArray"
attr(,"package")
[1] "SparseArray"
> dim(coo)
[1] 27 75  2
> 
> ## Sanity check:
> stopifnot(is(coo, "COO_SparseArray"), identical(a, as.array(coo)))
> 
> ## ---------------------------------------------------------------------
> ## 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::h5mread(fname0, "mm10/data", index))
   user  system elapsed 
  1.526   0.212   4.250 
> system.time(b <- h5read(fname0, "mm10/data", index=index))
   user  system elapsed 
 14.141   0.105  14.268 
> stopifnot(identical(a, as.vector(b)))
> 
> index <- list(sample(1306127, 7500, replace=TRUE))
> ## h5mread() is about 14x faster than h5read():
> system.time(a <- h5mread::h5mread(fname0, "mm10/barcodes", index))
   user  system elapsed 
  0.129   0.004   0.138 
> system.time(b <- h5read(fname0, "mm10/barcodes", index=index))
   user  system elapsed 
  5.711   0.080   5.803 
> stopifnot(identical(a, as.vector(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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
H5File-class 0.241   0.02   5.813
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/h5mread.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL h5mread
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘h5mread’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c H5File.c -o H5File.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c global_errmsg_buf.c -o global_errmsg_buf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c H5DSetDescriptor.c -o H5DSetDescriptor.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5dimscales.c -o h5dimscales.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c uaselection.c -o uaselection.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5mread_helpers.c -o h5mread_helpers.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5mread_startscounts.c -o h5mread_startscounts.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c TouchedChunks.c -o TouchedChunks.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5mread_index.c -o h5mread_index.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5mread_sparse.c -o h5mread_sparse.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5mread.c -o h5mread.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c h5summarize.c -o h5summarize.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c R_init_h5mread.c -o R_init_h5mread.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o h5mread.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o TouchedChunks.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_h5mread.o /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-h5mread/00new/h5mread/libs
** 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
** 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 (h5mread)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(h5mread)
Loading required package: rhdf5
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: SparseArray
Loading required package: Matrix
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


Attaching package: 'h5mread'

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

    h5ls

> 
> test_check("h5mread")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 18229 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-uaselection.R:55:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 18229 ]
> 
> proc.time()
   user  system elapsed 
108.239   3.886 112.359