##############################################################################
##############################################################################
###
### 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_1.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/h5mread.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘1.1.1’
* 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 ... 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 16.4Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     13.7Mb
* 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 ... 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/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)
File ‘h5mread/libs/h5mread.so’:
  Found non-API call to R: ‘DATAPTR’

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.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* 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: H5File-class
> ### Title: H5File objects
> ### Aliases: class:H5FileID H5FileID-class H5FileID open.H5FileID
> ###   close.H5FileID show,H5FileID-method class:H5File H5File-class H5File
> ###   path,H5File-method open.H5File close.H5File show,H5File-method
> ###   coerce,H5File,H5IdComponent-method class:character_OR_H5File
> ###   character_OR_H5File-class character_OR_H5File class:H5DSetDescriptor
> ###   H5DSetDescriptor-class H5DSetDescriptor destroy_H5DSetDescriptor
> ###   show,H5DSetDescriptor-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## A. BASIC USAGE
> ## ---------------------------------------------------------------------
> 
> ## With a local file:
> test_h5 <- system.file("extdata", "test.h5", package="h5mread")
> h5file1 <- H5File(test_h5)
> h5ls(h5file1)
          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
> path(h5file1)
[1] "/home/biocbuild/R/R-4.5.0/site-library/h5mread/extdata/test.h5"
> 
> h5mread(h5file1, "m2", list(1:10, 1:6))
            [,1]       [,2]       [,3]       [,4]       [,5]       [,6]
 [1,] -2.1242248         NA        NaN -2.5779525  1.9532461  4.9112339
 [2,]  2.8830514        Inf       -Inf -0.1996812 -1.2167090 -1.9776935
 [3,] -0.9102308  0.9364751  2.4219044  3.4048459  4.6469619 -0.6624099
 [4,]  3.8301740  3.0719664 -2.7439101  4.9207697  0.2735301 -3.3947909
 [5,]  4.4046728 -2.0594922  2.4889107 -2.5576531 -4.5567993  3.2302671
 [6,] -4.5444350 -3.5891478  3.2486851  1.2303872  1.7265274 -2.9190945
 [7,]  0.2810549  3.8862110 -4.0045662 -0.4121020  1.1311564 -2.1503403
 [8,]  3.9241904 -4.9171500 -2.2412863  3.4837234 -0.7017639  0.4620889
 [9,]  0.5143501  0.6912065 -4.7862322  2.2703366 -1.0607908  0.8904540
[10,] -0.4338526  4.6755019  0.9624297 -3.0869540  2.6021692 -0.5774682
> get_h5mread_returned_type(h5file1, "m2")
[1] "double"
> 
> ## 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"
+   h5file2 <- H5File(public_S3_url, s3=TRUE)
+   h5ls(h5file2)
+ 
+   h5mread(h5file2, "a1")
+   get_h5mread_returned_type(h5file2, "a1")
+ }
Error in .Call2("C_h5openS3file", filepath, auth, aws_region, secret_id,  : 
  Rhdf5lib was not compiled with support for the S3 VFD
Calls: H5File -> H5FileID -> .h5openfile -> .h5openS3file -> .Call2
Execution halted
* 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-3.22-bioc/meat/h5mread.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL h5mread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘h5mread’ ...
** this is package ‘h5mread’ version ‘1.1.1’
** 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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/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/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 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.

> 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 
107.695   4.620 112.741