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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_1.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Rarr.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rarr/DESCRIPTION’ ... OK
* this is package ‘Rarr’ version ‘1.7.1’
* 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 ... 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 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  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ...Warning: program compiled against libxml 212 using older 211
 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 ... 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 is not available
File ‘Rarr/libs/Rarr.so’:
  Found non-API call to R: ‘SETLENGTH’

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 ... 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-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-devel_2024-11-24/site-library’
* installing *source* package ‘Rarr’ ...
** using staged installation
NO_RLIB=
R_CPPFLAGS=-I/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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 -I"/home/biocbuild/R/R/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-3.21-bioc/meat/Rarr/src/compression_tools/zstd'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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-3.21-bioc/meat/Rarr/src/compression_tools/zstd'
make -C compression_tools/blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/Rarr/src/compression_tools/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.21-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/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/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/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/include -DUSING_R  -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.21-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-3.21-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 -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 -g -O2 -Wall -Werror=format-security -fPIC -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.21-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-3.21-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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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:316:22: warning: unused variable ‘cpu_features’ [-Wunused-variable]
  316 |   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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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 -g -O2 -Wall -Werror=format-security -fPIC -I/usr/local/include -I/home/biocbuild/R/R/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-3.21-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-3.21-bioc/meat/Rarr/src/compression_tools/blosc'
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o 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/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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.

> 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
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 10ms

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 10ms

test_decompression.R..........    0 tests    
test_decompression.R..........   15 tests OK 47ms

test_fill_values.R............    0 tests    
test_fill_values.R............    0 tests    
test_fill_values.R............   10 tests OK 19ms

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 26ms

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 22ms

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 30ms

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 21ms

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 41ms

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 21ms

test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    5 tests OK 5ms

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 59ms

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 1.0s

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

test_s3.R.....................    1 tests OK 0.3s

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 0.4s

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 12ms

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 76ms

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 18ms

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 12ms

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 33ms

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 10ms

test_utils.R..................    1 tests OK 
test_utils.R..................    2 tests OK 
test_utils.R..................    3 tests OK 4ms
All ok, 218 results (3.4s)
> 
> proc.time()
   user  system elapsed 
  9.325   0.679  10.244