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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1664/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rarr 1.6.0  (landing page)
Mike Smith
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/Rarr
git_branch: RELEASE_3_20
git_last_commit: 270345b
git_last_commit_date: 2024-10-29 11:19:41 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Rarr on kjohnson1

To the developers/maintainers of the Rarr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rarr.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rarr
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rarr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rarr_1.6.0.tar.gz
StartedAt: 2024-12-21 06:00:14 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 06:02:40 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 145.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Rarr.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rarr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rarr_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rarr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rarr/DESCRIPTION’ ... OK
* this is package ‘Rarr’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rarr’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* 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 ... 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 ... 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 ... NOTE
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 ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rarr/libs/Rarr.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rarr.Rcheck/00check.log’
for details.

Installation output

Rarr.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rarr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Rarr’ ...
** using staged installation
NO_RLIB=
R_CPPFLAGS=-I/Library/Frameworks/R.framework/Resources/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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c Rarr.c -o Rarr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c bit64_conversion.c -o bit64_conversion.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c compress.c -o compress.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c decompress.c -o decompress.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c float16_conversion.c -o float16_conversion.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c type_conversion.c -o type_conversion.o
make -C compression_tools/zstd
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -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 -C compression_tools/blosc
make -C lib/snappy-1.1.1
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -DUSING_R  -c snappy.cc
snappy.cc:578:13: warning: unused function 'ComputeTable' [-Wunused-function]
static void ComputeTable() {
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -DUSING_R  -c snappy-c.cc
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -DUSING_R  -c snappy-sinksource.cc
clang++ -arch arm64 -std=gnu++17 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -DUSING_R  -c snappy-stubs-internal.cc
make -C lib/lz4-1.9.2
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -DNLZ4_DEBUG -c lz4.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -DNLZ4_DEBUG -c lz4hc.c
make -C lib/blosc-1.20.1 all
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c bitshuffle-generic.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c shuffle-generic.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R    -c shuffle.c
shuffle.c:316:22: warning: unused variable 'cpu_features' [-Wunused-variable]
  blosc_cpu_features cpu_features = blosc_get_cpu_features();
                     ^
In file included from shuffle.c:12:
./shuffle-generic.h:32:13: warning: unused function 'shuffle_generic_inline' [-Wunused-function]
static void shuffle_generic_inline(const size_t type_size,
            ^
./shuffle-generic.h:61:13: warning: unused function 'unshuffle_generic_inline' [-Wunused-function]
static void unshuffle_generic_inline(const size_t type_size,
            ^
3 warnings generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c blosclz.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c blosc.c
blosc.c:742:11: warning: variable 'ctbytes' set but not used [-Wunused-but-set-variable]
  int32_t ctbytes = 0;           /* number of compressed bytes in block */
          ^
blosc.c:303:12: warning: unused function 'compname_to_clibcode' [-Wunused-function]
static int compname_to_clibcode(const char *compname)
           ^
2 warnings generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c fastcopy.c
fastcopy.c:69:30: warning: unused function 'copy_5_bytes' [-Wunused-function]
static inline unsigned char *copy_5_bytes(unsigned char *out, const unsigned char *from) {
                             ^
fastcopy.c:74:30: warning: unused function 'copy_6_bytes' [-Wunused-function]
static inline unsigned char *copy_6_bytes(unsigned char *out, const unsigned char *from) {
                             ^
fastcopy.c:79:30: warning: unused function 'copy_7_bytes' [-Wunused-function]
static inline unsigned char *copy_7_bytes(unsigned char *out, const unsigned char *from) {
                             ^
3 warnings generated.
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
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

Tests output

Rarr.Rcheck/tests/tinytest.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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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
'help.start()' for an HTML browser interface to help.
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> 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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_argument_handling.R......    1 tests OK 0.3s

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 21ms

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 7ms

test_decompression.R..........    0 tests    
test_decompression.R..........   15 tests OK 25ms

test_fill_values.R............    0 tests    
test_fill_values.R............    0 tests    
test_fill_values.R............   10 tests OK 16ms

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 16ms

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 16ms

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 14ms

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 15ms

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 26ms

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 15ms

test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    0 tests    
test_normalize_path.R.........    5 tests OK 4ms

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 12ms

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 3.7s

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

test_s3.R.....................    1 tests OK 0.1s

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 0.3s

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 10ms

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 22ms

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 11ms

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 8ms

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 26ms

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 7ms

test_utils.R..................    1 tests OK 
test_utils.R..................    2 tests OK 
test_utils.R..................    3 tests OK 3ms
All ok, 213 results (4.7s)
> 
> proc.time()
   user  system elapsed 
  7.925   2.706  10.681

Example timings

Rarr.Rcheck/Rarr-Ex.timings

nameusersystemelapsed
compressors0.3480.0780.428
create_empty_zarr_array0.0020.0010.002
read_zarr_array0.0150.0310.047
update_zarr_array0.0070.0020.009
write_zarr_array0.0040.0020.006
zarr_overview0.1160.0162.542