##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:h5mread.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings h5mread_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/h5mread.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-13 04:01:45 UTC
* checking for file ‘h5mread/DESCRIPTION’ ... OK
* this is package ‘h5mread’ version ‘1.3.2’
* 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 ... WARNING
Found the following significant warnings:
  H5DSetDescriptor.c:1192:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  H5DSetDescriptor.c:1202:38: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  TouchedChunks.c:312:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  TouchedChunks.c:569:35: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  TouchedChunks.c:569:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/h5mread.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... INFO
  installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs     12.6Mb
* 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 ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/h5mread/libs/h5mread.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
h5mread 57.756   5.12   66.19
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/h5mread.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL h5mread
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘h5mread’ ...
** this is package ‘h5mread’ version ‘1.3.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5File.c -o H5File.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c: In function ‘C_show_H5DSetDescriptor_xp’:
H5DSetDescriptor.c:1192:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
 1192 |                 Rprintf(" %llu", h5dset->h5dim[h5along]);
      |                           ~~~^   ~~~~~~~~~~~~~~~~~~~~~~
      |                              |                |
      |                              |                hsize_t {aka long unsigned int}
      |                              long long unsigned int
      |                           %lu
H5DSetDescriptor.c:1202:38: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
 1202 |                         Rprintf(" %llu",
      |                                   ~~~^
      |                                      |
      |                                      long long unsigned int
      |                                   %lu
 1203 |                                 h5dset->h5chunkdim[h5along]);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                   |
      |                                                   hsize_t {aka long unsigned int}
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5dimscales.c -o h5dimscales.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c uaselection.c -o uaselection.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_helpers.c -o h5mread_helpers.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c TouchedChunks.c -o TouchedChunks.o
In file included from TouchedChunks.c:9:
TouchedChunks.c: In function ‘read_h5chunk’:
TouchedChunks.c:312:37: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  312 |                 PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  313 |                                     "than expected (%llu + %d)",
  314 |                                     chunk_storage_size,
      |                                     ~~~~~~~~~~~~~~~~~~
      |                                     |
      |                                     hsize_t {aka long unsigned int}
global_errmsg_buf.h:9:67: note: in definition of macro ‘PRINT_TO_ERRMSG_BUF’
    9 |         snprintf(_h5mread_global_errmsg_buf(), ERRMSG_BUF_LENGTH, __VA_ARGS__)
      |                                                                   ^~~~~~~~~~~
TouchedChunks.c:312:61: note: format string is defined here
  312 |                 PRINT_TO_ERRMSG_BUF("chunk storage size (%llu) bigger "
      |                                                          ~~~^
      |                                                             |
      |                                                             long long unsigned int
      |                                                          %lu
TouchedChunks.c: In function ‘_print_tchunk_info’:
TouchedChunks.c:569:35: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  569 |                 Rprintf("#%lld=%llu:%llu", tchunkidx + 1,
      |                                ~~~^
      |                                   |
      |                                   long long unsigned int
      |                                %lu
  570 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |
      |                                                                           hsize_t {aka long unsigned int}
TouchedChunks.c:569:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
  569 |                 Rprintf("#%lld=%llu:%llu", tchunkidx + 1,
      |                                     ~~~^
      |                                        |
      |                                        long long unsigned int
      |                                     %lu
  570 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] + 1,
  571 |                         tchunk_iter->tchunk_vps.h5chunk_vp.h5off[h5along] +
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                           |
      |                                                                           hsize_t {aka long unsigned int}
  572 |                             tchunk_iter->tchunk_vps.h5chunk_vp.h5dim[h5along]);
      |                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_index.c -o h5mread_index.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread_sparse.c -o h5mread_sparse.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5mread.c -o h5mread.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c h5summarize.c -o h5summarize.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/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
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/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/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

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'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 
 76.099   1.960  78.571