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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:Rarr.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Rarr_1.9.17.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Rarr.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 ‘Rarr/DESCRIPTION’ ... OK
* this is package ‘Rarr’ version ‘1.9.17’
* 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:
  .lintr
  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/metadata/consolidated.zarr/.zattrs
  inst/extdata/zarr_examples/metadata/consolidated.zarr/.zgroup
  inst/extdata/zarr_examples/metadata/consolidated.zarr/.zmetadata
  inst/extdata/zarr_examples/metadata/consolidated.zarr/a/.zarray
  inst/extdata/zarr_examples/metadata/consolidated.zarr/a/.zattrs
  inst/extdata/zarr_examples/metadata/consolidated.zarr/b/.zarray
  inst/extdata/zarr_examples/metadata/consolidated.zarr/b/.zattrs
  inst/extdata/zarr_examples/metadata/consolidated.zarr/c/.zarray
  inst/extdata/zarr_examples/metadata/consolidated.zarr/c/.zattrs
  inst/extdata/zarr_examples/metadata/invalid_mixed.zarr/.zarray
  inst/extdata/zarr_examples/metadata/invalid_mixed.zarr/.zattrs
  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/other.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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rarr’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      5.5Mb
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.file_or_blob_exists: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/Rarr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Rarr
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Rarr’ ...
** this is package ‘Rarr’ version ‘1.9.17’
** using staged installation
NO_RLIB=
R_CPPFLAGS=-I/home/biocbuild/R/R-4.5.0/include
configure: is Bioc build machine
configure: configuring the Zstd filter...
configure: compiling bundled Zstd library
configure: configuring the BLOSC filter...
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... no
configure: Bioc build machine; disabling MAVX2
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/compression_tools/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/compression_tools/blosc/Makefile
config.status: creating src/compression_tools/blosc/lib/snappy-1.1.1/Makefile
** 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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c Rarr.c -o Rarr.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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c bit64_conversion.c -o bit64_conversion.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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c compress.c -o compress.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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c decompress.c -o decompress.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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c float16_conversion.c -o float16_conversion.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/usr/local/include  -I/usr/local/include   -g -O2 -Wall -Werror=format-security -fPIC  -g -O2  -Wall -Werror=format-security -c type_conversion.c -o type_conversion.o
make -C compression_tools/zstd
make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/zstd'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -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 '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/zstd'
make -C compression_tools/blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -DUSING_R  -c snappy.cc
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::Append(const char*, size_t)’:
snappy.cc:1021:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1021 |         if (curr_iov_index_ + 1 >= output_iov_count_) {
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)’:
snappy.cc:1103:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1103 |           if (curr_iov_index_ + 1 >= output_iov_count_) {
      |               ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: At global scope:
snappy.cc:578:13: warning: ‘void snappy::ComputeTable()’ defined but not used [-Wunused-function]
  578 | static void ComputeTable() {
      |             ^~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -DUSING_R  -c snappy-c.cc
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -DUSING_R  -c snappy-sinksource.cc
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -DUSING_R  -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.2
make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -DNLZ4_DEBUG -c lz4.c
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c bitshuffle-generic.c
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c shuffle-generic.c
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R    -c shuffle.c
shuffle.c: In function ‘get_shuffle_implementation’:
shuffle.c:318:22: warning: unused variable ‘cpu_features’ [-Wunused-variable]
  318 |   blosc_cpu_features cpu_features = blosc_get_cpu_features();
      |                      ^~~~~~~~~~~~
In file included from shuffle.c:12:
shuffle-generic.h: At top level:
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,
      |             ^~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c blosclz.c
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -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)
      |            ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.5.0/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c fastcopy.c
make[2]: Leaving directory '/home/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/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.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 '/home/biocbuild/bbs-3.22-bioc/meat/Rarr/src/compression_tools/blosc'
/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 Rarr.so 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 -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-Rarr/00new/Rarr/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 (Rarr)

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.

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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
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(Rarr)
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: DelayedArray
Loading required package: stats4
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

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    expand, unname

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

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

> 
> test_check("Rarr")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 6 | PASS 252 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test-attributes.R:150:3', 'test-read_metadata.R:25:3',
  'test-read_metadata.R:67:3', 'test-read_metadata.R:97:3',
  'test-read_metadata.R:128:3', 'test-s3.R:14:3'

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 252 ]
> 
> proc.time()
   user  system elapsed 
 30.468   2.515  21.324