##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rarr.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings Rarr_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/Rarr.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rarr/DESCRIPTION' ... OK
* this is package 'Rarr' version '1.9.0'
* 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:
  inst/extdata/zarr_examples/column-first/Unicode.zarr/.zarray
  inst/extdata/zarr_examples/column-first/boolean.zarr/.zarray
  inst/extdata/zarr_examples/column-first/float16.zarr/.zarray
  inst/extdata/zarr_examples/column-first/float32.zarr/.zarray
  inst/extdata/zarr_examples/column-first/float64.zarr/.zarray
  inst/extdata/zarr_examples/column-first/int16.zarr/.zarray
  inst/extdata/zarr_examples/column-first/int32.zarr/.zarray
  inst/extdata/zarr_examples/column-first/int64.zarr/.zarray
  inst/extdata/zarr_examples/column-first/int8.zarr/.zarray
  inst/extdata/zarr_examples/column-first/string.zarr/.zarray
  inst/extdata/zarr_examples/column-first/uint16.zarr/.zarray
  inst/extdata/zarr_examples/column-first/uint32.zarr/.zarray
  inst/extdata/zarr_examples/column-first/uint64.zarr/.zarray
  inst/extdata/zarr_examples/column-first/uint8.zarr/.zarray
  inst/extdata/zarr_examples/column-first/vlenUTF8.zarr/.zarray
  inst/extdata/zarr_examples/compression/bzip2.zarr/.zarray
  inst/extdata/zarr_examples/compression/lz4.zarr/.zarray
  inst/extdata/zarr_examples/compression/lzma.zarr/.zarray
  inst/extdata/zarr_examples/compression/zlib.zarr/.zarray
  inst/extdata/zarr_examples/compression/zstd.zarr/.zarray
  inst/extdata/zarr_examples/fill-values/double-inf.zarr/.zarray
  inst/extdata/zarr_examples/fill-values/double-neginf.zarr/.zarray
  inst/extdata/zarr_examples/row-first/float16.zarr/.zarray
  inst/extdata/zarr_examples/row-first/float32.zarr/.zarray
  inst/extdata/zarr_examples/row-first/float64.zarr/.zarray
  inst/extdata/zarr_examples/row-first/int16.zarr/.zarray
  inst/extdata/zarr_examples/row-first/int32.zarr/.zarray
  inst/extdata/zarr_examples/row-first/int64.zarr/.zarray
  inst/extdata/zarr_examples/row-first/int8.zarr/.zarray
  inst/extdata/zarr_examples/row-first/string.zarr/.zarray
  inst/extdata/zarr_examples/row-first/uint32.zarr/.zarray
  inst/extdata/zarr_examples/row-first/uint64.zarr/.zarray
  inst/extdata/zarr_examples/row-first/uint8.zarr/.zarray
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rarr' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 14.2.0'
* checking installed package size ... OK
* 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 dependencies in R code ... OK
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ZarrRealizationSink.Rd: RealizationSink-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 shell scripts ... 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.22-bioc/R/library/Rarr/libs/x64/Rarr.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/Rarr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL Rarr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'Rarr' ...
** this is package 'Rarr' version '1.9.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c Rarr.c -o Rarr.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c bit64_conversion.c -o bit64_conversion.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c compress.c -o compress.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c decompress.c -o decompress.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c float16_conversion.c -o float16_conversion.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG     -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c type_conversion.c -o type_conversion.o
/usr/bin/make -C compression_tools/zstd
make[1]: Entering directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/zstd'
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
rm -f libzstd.a
ar cq libzstd.a common/debug.o common/entropy_common.o common/error_private.o common/fse_decompress.o common/pool.o common/threading.o common/xxhash.o common/zstd_common.o compress/fse_compress.o compress/hist.o compress/huf_compress.o compress/zstd_compress.o compress/zstd_compress_literals.o compress/zstd_compress_sequences.o compress/zstd_compress_superblock.o compress/zstd_double_fast.o compress/zstd_fast.o compress/zstd_lazy.o compress/zstd_ldm.o compress/zstd_opt.o compress/zstdmt_compress.o decompress/huf_decompress.o decompress/zstd_ddict.o decompress/zstd_decompress.o decompress/zstd_decompress_block.o
ranlib libzstd.a
make[1]: Leaving directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/zstd'
/usr/bin/make -C compression_tools/blosc
make[1]: Entering directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc'
/usr/bin/make -C lib/snappy-1.1.1
make[2]: Entering directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17     -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -DUSING_R  -c snappy.cc
g++ -std=gnu++17     -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -DUSING_R  -c snappy-c.cc
g++ -std=gnu++17     -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -DUSING_R  -c snappy-sinksource.cc
g++ -std=gnu++17     -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -DUSING_R  -c snappy-stubs-internal.cc
make[2]: Leaving directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
/usr/bin/make -C lib/lz4-1.9.2
make[2]: Entering directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -DNLZ4_DEBUG -c lz4.c
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign  -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
/usr/bin/make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c bitshuffle-sse2.c
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_byte_elem_sse2':
bitshuffle-sse2.c:260:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  260 | }
      | ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_bit_elem_sse2':
bitshuffle-sse2.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  308 | }
      | ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_byte_bitrow_sse2':
bitshuffle-sse2.c:414:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  414 | }
      | ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_sse2':
bitshuffle-sse2.c:451:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  451 | }
      | ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_untrans_bit_elem_sse2':
bitshuffle-sse2.c:467:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  467 | }
      | ^
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c shuffle-sse2.c
shuffle-sse2.c: In function 'blosc_internal_shuffle_sse2':
shuffle-sse2.c:568:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  568 | }
      | ^
shuffle-sse2.c: In function 'blosc_internal_unshuffle_sse2':
shuffle-sse2.c:626:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  626 | }
      | ^
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c bitshuffle-generic.c
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder':
bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   40 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal':
bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   48 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder':
bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   85 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem':
bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  109 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight':
bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  121 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal':
bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  139 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal':
bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  204 | }
      | ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal':
bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  220 | }
      | ^
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c shuffle-generic.c
shuffle-generic.c: In function 'blosc_internal_shuffle_generic':
shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   17 | }
      | ^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
   25 | }
      | ^
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -DSHUFFLE_SSE2_ENABLED  -c shuffle.c
In file included from shuffle.c:12:
shuffle-generic.h:61:13: warning: 'unshuffle_generic_inline' defined but not used [-Wunused-function]
   61 | static void unshuffle_generic_inline(const size_t type_size,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~
shuffle-generic.h:32:13: warning: 'shuffle_generic_inline' defined but not used [-Wunused-function]
   32 | static void shuffle_generic_inline(const size_t type_size,
      |             ^~~~~~~~~~~~~~~~~~~~~~
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:392:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  392 | }
      | ^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:405:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  405 | }
      | ^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:432:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  432 | }
      | ^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:459:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
  459 | }
      | ^
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c blosclz.c
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c blosc.c
blosc.c:303:12: warning: 'compname_to_clibcode' defined but not used [-Wunused-function]
  303 | static int compname_to_clibcode(const char *compname)
      |            ^~~~~~~~~~~~~~~~~~~~
blosc.c:156:16: warning: 'g_atfork_registered' defined but not used [-Wunused-variable]
  156 | static int32_t g_atfork_registered = 0;
      |                ^~~~~~~~~~~~~~~~~~~
gcc  -O2 -Wall -std=gnu2x -mfpmath=sse -msse2 -mstackrealign   -IF:/biocbuild/bbs-3.22-bioc/R/include -IF:/biocbuild/bbs-3.22-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd -msse2  -DUSING_R  -c fastcopy.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-sse2.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/bitshuffle-sse2.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o
ranlib libblosc.a
make[1]: Leaving directory '/f/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc'
gcc -shared -s -static-libgcc -o Rarr.dll tmp.def Rarr.o bit64_conversion.o compress.o decompress.o float16_conversion.o type_conversion.o compression_tools/blosc/libblosc.a compression_tools/zstd/libzstd.a -lz -lstdc++ -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-Rarr/00new/Rarr/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rarr)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> if (requireNamespace("tinytest", quietly = TRUE)) {
+   tinytest::test_package("Rarr")
+ }
Loading required package: DelayedArray
Loading required package: stats4
Loading required package: Matrix
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: 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

Attaching package: 'IRanges'

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

    windows

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


test_ZarrArray-class.R........    0 tests    
test_ZarrArray-class.R........    0 tests    
test_ZarrArray-class.R........    0 tests    
test_ZarrArray-class.R........    0 tests    
test_ZarrArray-class.R........    1 tests OK 
test_ZarrArray-class.R........    2 tests OK 
test_ZarrArray-class.R........    3 tests OK 
test_ZarrArray-class.R........    4 tests OK 
test_ZarrArray-class.R........    5 tests OK 1.2s

test_argument_handling.R......    1 tests OK 4ms

test_boolean.R................    0 tests    
test_boolean.R................    0 tests    
test_boolean.R................    1 tests OK 
test_boolean.R................    2 tests OK 
test_boolean.R................    3 tests OK 
test_boolean.R................    4 tests OK 
test_boolean.R................    5 tests OK 8ms

test_datatypes.R..............    1 tests OK 
test_datatypes.R..............    2 tests OK 
test_datatypes.R..............    3 tests OK 
test_datatypes.R..............    4 tests OK 
test_datatypes.R..............    5 tests OK 
test_datatypes.R..............    6 tests OK 
test_datatypes.R..............    7 tests OK 
test_datatypes.R..............    8 tests OK 
test_datatypes.R..............    9 tests OK 
test_datatypes.R..............   10 tests OK 
test_datatypes.R..............   11 tests OK 
test_datatypes.R..............   12 tests OK 
test_datatypes.R..............   13 tests OK 
test_datatypes.R..............   14 tests OK 
test_datatypes.R..............   15 tests OK 
test_datatypes.R..............   16 tests OK 6ms

test_decompression.R..........    0 tests    
test_decompression.R..........   15 tests OK 33ms

test_fill_values.R............    0 tests    
test_fill_values.R............    0 tests    
test_fill_values.R............   10 tests OK 18ms

test_float16.R................    0 tests    
test_float16.R................    0 tests    
test_float16.R................    0 tests    
test_float16.R................    1 tests OK 
test_float16.R................    2 tests OK 
test_float16.R................    3 tests OK 
test_float16.R................    4 tests OK 
test_float16.R................    5 tests OK 
test_float16.R................    6 tests OK 
test_float16.R................    7 tests OK 
test_float16.R................    8 tests OK 
test_float16.R................    9 tests OK 20ms

test_float32.R................    0 tests    
test_float32.R................    0 tests    
test_float32.R................    0 tests    
test_float32.R................    1 tests OK 
test_float32.R................    2 tests OK 
test_float32.R................    3 tests OK 
test_float32.R................    4 tests OK 
test_float32.R................    5 tests OK 
test_float32.R................    6 tests OK 
test_float32.R................    7 tests OK 17ms

test_float64.R................    0 tests    
test_float64.R................    0 tests    
test_float64.R................    0 tests    
test_float64.R................    1 tests OK 
test_float64.R................    2 tests OK 
test_float64.R................    3 tests OK 
test_float64.R................    4 tests OK 
test_float64.R................    5 tests OK 
test_float64.R................    6 tests OK 
test_float64.R................    7 tests OK 19ms

test_int16.R..................    0 tests    
test_int16.R..................    0 tests    
test_int16.R..................    0 tests    
test_int16.R..................    1 tests OK 
test_int16.R..................    2 tests OK 
test_int16.R..................    3 tests OK 
test_int16.R..................    4 tests OK 
test_int16.R..................    5 tests OK 
test_int16.R..................    6 tests OK 
test_int16.R..................    7 tests OK 17ms

test_int32.R..................    0 tests    
test_int32.R..................    0 tests    
test_int32.R..................    0 tests    
test_int32.R..................    1 tests OK 
test_int32.R..................    2 tests OK 
test_int32.R..................    3 tests OK 
test_int32.R..................    4 tests OK 
test_int32.R..................    5 tests OK 
test_int32.R..................    6 tests OK 
test_int32.R..................    7 tests OK 20ms

test_int64.R..................    0 tests    
test_int64.R..................    0 tests    
test_int64.R..................    0 tests    
test_int64.R..................    1 tests OK 
test_int64.R..................    2 tests OK 
test_int64.R..................    3 tests OK 
test_int64.R..................    4 tests OK 
test_int64.R..................    5 tests OK 
test_int64.R..................    6 tests OK 
test_int64.R..................    7 tests OK 
test_int64.R..................    8 tests OK 
test_int64.R..................    9 tests OK 
test_int64.R..................   10 tests OK 
test_int64.R..................   11 tests OK 
test_int64.R..................   12 tests OK 
test_int64.R..................   13 tests OK 
test_int64.R..................   14 tests OK 
test_int64.R..................   15 tests OK 46ms

test_int8.R...................    0 tests    
test_int8.R...................    0 tests    
test_int8.R...................    0 tests    
test_int8.R...................    1 tests OK 
test_int8.R...................    2 tests OK 
test_int8.R...................    3 tests OK 
test_int8.R...................    4 tests OK 
test_int8.R...................    5 tests OK 
test_int8.R...................    6 tests OK 
test_int8.R...................    7 tests OK 20ms

test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    3 tests OK 3ms

test_read_metadata.R..........    0 tests    
test_read_metadata.R..........    0 tests    
test_read_metadata.R..........    1 tests OK 
test_read_metadata.R..........    2 tests OK 
test_read_metadata.R..........    3 tests OK 11ms

test_roundtrip.R..............    0 tests    
test_roundtrip.R..............    1 tests OK 
test_roundtrip.R..............    2 tests OK 
test_roundtrip.R..............    3 tests OK 
test_roundtrip.R..............    3 tests OK 
test_roundtrip.R..............    3 tests OK 
test_roundtrip.R..............    4 tests OK 
test_roundtrip.R..............    5 tests OK 
test_roundtrip.R..............    5 tests OK 
test_roundtrip.R..............    6 tests OK 
test_roundtrip.R..............    7 tests OK 
test_roundtrip.R..............    7 tests OK 
test_roundtrip.R..............    8 tests OK 
test_roundtrip.R..............    9 tests OK 
test_roundtrip.R..............    9 tests OK 
test_roundtrip.R..............   10 tests OK 
test_roundtrip.R..............   11 tests OK 
test_roundtrip.R..............   11 tests OK 
test_roundtrip.R..............   12 tests OK 
test_roundtrip.R..............   13 tests OK 
test_roundtrip.R..............   13 tests OK 
test_roundtrip.R..............   14 tests OK 
test_roundtrip.R..............   15 tests OK 
test_roundtrip.R..............   15 tests OK 
test_roundtrip.R..............   16 tests OK 
test_roundtrip.R..............   17 tests OK 
test_roundtrip.R..............   17 tests OK 
test_roundtrip.R..............   18 tests OK 
test_roundtrip.R..............   19 tests OK 
test_roundtrip.R..............   19 tests OK 
test_roundtrip.R..............   20 tests OK 
test_roundtrip.R..............   21 tests OK 
test_roundtrip.R..............   21 tests OK 
test_roundtrip.R..............   22 tests OK 
test_roundtrip.R..............   23 tests OK 15.7s

test_s3.R.....................    0 tests    
test_s3.R.....................    0 tests    Loading required package: mockery

test_s3.R.....................    1 tests OK 0.2s

test_string.R.................    0 tests    
test_string.R.................    0 tests    
test_string.R.................    0 tests    
test_string.R.................    1 tests OK 
test_string.R.................    2 tests OK 
test_string.R.................    3 tests OK 
test_string.R.................    4 tests OK 
test_string.R.................    5 tests OK 
test_string.R.................    6 tests OK 
test_string.R.................    7 tests OK 
test_string.R.................    7 tests OK 
test_string.R.................    8 tests OK 
test_string.R.................    9 tests OK 
test_string.R.................    9 tests OK 
test_string.R.................   10 tests OK 
test_string.R.................   11 tests OK 
test_string.R.................   11 tests OK 
test_string.R.................   11 tests OK 
test_string.R.................   12 tests OK 
test_string.R.................   13 tests OK 
test_string.R.................   14 tests OK 
test_string.R.................   14 tests OK 
test_string.R.................   15 tests OK 
test_string.R.................   16 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   17 tests OK 
test_string.R.................   18 tests OK 0.5s

test_uint16.R.................    0 tests    
test_uint16.R.................    0 tests    
test_uint16.R.................    1 tests OK 
test_uint16.R.................    2 tests OK 
test_uint16.R.................    3 tests OK 
test_uint16.R.................    4 tests OK 
test_uint16.R.................    5 tests OK 16ms

test_uint32.R.................    0 tests    
test_uint32.R.................    0 tests    
test_uint32.R.................    0 tests    
test_uint32.R.................    1 tests OK 
test_uint32.R.................    2 tests OK 
test_uint32.R.................    3 tests OK 
test_uint32.R.................    4 tests OK 
test_uint32.R.................    5 tests OK 
test_uint32.R.................    6 tests OK 
test_uint32.R.................    7 tests OK 
test_uint32.R.................    8 tests OK 
test_uint32.R.................    9 tests OK 
test_uint32.R.................   10 tests OK 
test_uint32.R.................   11 tests OK 38ms

test_uint64.R.................    0 tests    
test_uint64.R.................    0 tests    
test_uint64.R.................    1 tests OK 
test_uint64.R.................    2 tests OK 
test_uint64.R.................    3 tests OK 
test_uint64.R.................    4 tests OK 
test_uint64.R.................    5 tests OK 
test_uint64.R.................    6 tests OK 
test_uint64.R.................    7 tests OK 21ms

test_uint8.R..................    0 tests    
test_uint8.R..................    0 tests    
test_uint8.R..................    1 tests OK 
test_uint8.R..................    2 tests OK 
test_uint8.R..................    3 tests OK 
test_uint8.R..................    4 tests OK 
test_uint8.R..................    5 tests OK 16ms

test_update_zarr.R............    0 tests    
test_update_zarr.R............    0 tests    
test_update_zarr.R............    0 tests    
test_update_zarr.R............    1 tests OK 
test_update_zarr.R............    2 tests OK 
test_update_zarr.R............    3 tests OK 
test_update_zarr.R............    3 tests OK 
test_update_zarr.R............    4 tests OK 
test_update_zarr.R............    5 tests OK 
test_update_zarr.R............    6 tests OK 
test_update_zarr.R............    6 tests OK 
test_update_zarr.R............    6 tests OK 
test_update_zarr.R............    6 tests OK 
test_update_zarr.R............    6 tests OK 
test_update_zarr.R............    7 tests OK 
test_update_zarr.R............    8 tests OK 0.1s

test_url_parsing.R............    0 tests    
test_url_parsing.R............   10 tests OK 
test_url_parsing.R............   15 tests OK 
test_url_parsing.R............   16 tests OK 
test_url_parsing.R............   17 tests OK 
test_url_parsing.R............   18 tests OK 13ms

test_utils.R..................    1 tests OK 
test_utils.R..................    2 tests OK 
test_utils.R..................    3 tests OK 5ms
All ok, 216 results (18.2s)
> 
> proc.time()
   user  system elapsed 
   9.21    2.67   25.17