Mike Smith
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/Rarr |
| git_branch: RELEASE_3_18 |
| git_last_commit: e9d1a91 |
| git_last_commit_date: 2023-10-24 11:48:08 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:10 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1661/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rarr 1.2.0 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: Rarr |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rarr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Rarr_1.2.0.tar.gz |
| StartedAt: 2024-04-16 04:07:14 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 04:08:08 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 53.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rarr.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rarr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Rarr_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/Rarr.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rarr/DESCRIPTION' ... OK
* this is package 'Rarr' version '1.2.0'
* 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/fill-values/double-inf.zarr/.zarray
inst/extdata/zarr_examples/fill-values/double-neginf.zarr/.zarray
inst/extdata/zarr_examples/row-first/float16.zarr/.zarray
inst/extdata/zarr_examples/row-first/float32.zarr/.zarray
inst/extdata/zarr_examples/row-first/float64.zarr/.zarray
inst/extdata/zarr_examples/row-first/int16.zarr/.zarray
inst/extdata/zarr_examples/row-first/int32.zarr/.zarray
inst/extdata/zarr_examples/row-first/int64.zarr/.zarray
inst/extdata/zarr_examples/row-first/int8.zarr/.zarray
inst/extdata/zarr_examples/row-first/string.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint32.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint64.zarr/.zarray
inst/extdata/zarr_examples/row-first/uint8.zarr/.zarray
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rarr' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/Rarr/libs/x64/Rarr.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'tinytest.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.18-bioc/meat/Rarr.Rcheck/00check.log'
for details.
Rarr.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL Rarr
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'Rarr' ...
** using staged installation
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture
using C compiler: 'gcc.exe (GCC) 12.3.0'
/usr/bin/make -C compression_tools/blosc
make[1]: Entering directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc'
/usr/bin/make -C lib/snappy-1.1.1
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -DUSING_R -c snappy.cc
g++ -std=gnu++17 -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -DUSING_R -c snappy-c.cc
g++ -std=gnu++17 -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -DUSING_R -c snappy-sinksource.cc
g++ -std=gnu++17 -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -DUSING_R -c snappy-stubs-internal.cc
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
/usr/bin/make -C lib/lz4-1.9.2
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DNLZ4_DEBUG -c lz4.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
/usr/bin/make -C lib/zstd-1.4.5
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/debug.c -o common/debug.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/entropy_common.c -o common/entropy_common.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/error_private.c -o common/error_private.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/fse_decompress.c -o common/fse_decompress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/threading.c -o common/threading.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/xxhash.c -o common/xxhash.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/zstd_common.c -o common/zstd_common.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/fse_compress.c -o compress/fse_compress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/hist.c -o compress/hist.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/huf_compress.c -o compress/huf_compress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
/usr/bin/make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c bitshuffle-sse2.c
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_byte_elem_sse2':
bitshuffle-sse2.c:260:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
260 | }
| ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_bit_elem_sse2':
bitshuffle-sse2.c:308:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
308 | }
| ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_trans_byte_bitrow_sse2':
bitshuffle-sse2.c:414:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
414 | }
| ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_sse2':
bitshuffle-sse2.c:451:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
451 | }
| ^
bitshuffle-sse2.c: In function 'blosc_internal_bshuf_untrans_bit_elem_sse2':
bitshuffle-sse2.c:467:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
467 | }
| ^
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c shuffle-sse2.c
shuffle-sse2.c: In function 'blosc_internal_shuffle_sse2':
shuffle-sse2.c:570:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
570 | }
| ^
shuffle-sse2.c: In function 'blosc_internal_unshuffle_sse2':
shuffle-sse2.c:628:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
628 | }
| ^
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c bitshuffle-generic.c
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder':
bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
40 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal':
bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
48 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder':
bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
85 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem':
bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
109 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight':
bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
121 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal':
bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
139 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal':
bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
204 | }
| ^
bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal':
bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
220 | }
| ^
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c shuffle-generic.c
shuffle-generic.c: In function 'blosc_internal_shuffle_generic':
shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
17 | }
| ^
shuffle-generic.c: In function 'blosc_internal_unshuffle_generic':
shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
25 | }
| ^
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -DSHUFFLE_SSE2_ENABLED -c shuffle.c
In file included from shuffle.c:12:
shuffle-generic.h:61:13: warning: 'unshuffle_generic_inline' defined but not used [-Wunused-function]
61 | static void unshuffle_generic_inline(const size_t type_size,
| ^~~~~~~~~~~~~~~~~~~~~~~~
shuffle-generic.h:32:13: warning: 'shuffle_generic_inline' defined but not used [-Wunused-function]
32 | static void shuffle_generic_inline(const size_t type_size,
| ^~~~~~~~~~~~~~~~~~~~~~
shuffle.c: In function 'blosc_internal_shuffle':
shuffle.c:392:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
392 | }
| ^
shuffle.c: In function 'blosc_internal_unshuffle':
shuffle.c:405:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
405 | }
| ^
shuffle.c: In function 'blosc_internal_bitshuffle':
shuffle.c:432:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
432 | }
| ^
shuffle.c: In function 'blosc_internal_bitunshuffle':
shuffle.c:459:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes]
459 | }
| ^
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c blosclz.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c blosc.c
blosc.c:305:12: warning: 'compname_to_clibcode' defined but not used [-Wunused-function]
305 | static int compname_to_clibcode(const char *compname)
| ^~~~~~~~~~~~~~~~~~~~
blosc.c:158:16: warning: 'g_atfork_registered' defined but not used [-Wunused-variable]
158 | static int32_t g_atfork_registered = 0;
| ^~~~~~~~~~~~~~~~~~~
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -IF:/biocbuild/bbs-3.18-bioc/R/include -IF:/biocbuild/bbs-3.18-bioc/R/include/x64 -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -DUSING_R -c fastcopy.c
make[2]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-sse2.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/bitshuffle-sse2.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
ranlib libblosc.a
make[1]: Leaving directory '/f/biocbuild/bbs-3.18-bioc/meat/Rarr/src/compression_tools/blosc'
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rarr.c -o Rarr.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bit64_conversion.c -o bit64_conversion.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c compress.c -o compress.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c decompress.c -o decompress.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c float16_conversion.c -o float16_conversion.o
gcc -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c type_conversion.c -o type_conversion.o
gcc -shared -s -static-libgcc -o Rarr.dll tmp.def Rarr.o bit64_conversion.o compress.o decompress.o float16_conversion.o type_conversion.o compression_tools/blosc/libblosc.a -lz -lstdc++ -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-Rarr/00new/Rarr/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rarr)
Rarr.Rcheck/tests/tinytest.Rout
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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")
+ }
test_argument_handling.R...... 1 tests [0;32mOK[0m [0;36m96ms[0m
test_boolean.R................ 0 tests
test_boolean.R................ 0 tests
test_boolean.R................ 1 tests [0;32mOK[0m
test_boolean.R................ 2 tests [0;32mOK[0m
test_boolean.R................ 3 tests [0;32mOK[0m
test_boolean.R................ 4 tests [0;32mOK[0m
test_boolean.R................ 5 tests [0;32mOK[0m [0;36m13ms[0m
test_datatypes.R.............. 1 tests [0;32mOK[0m
test_datatypes.R.............. 2 tests [0;32mOK[0m
test_datatypes.R.............. 3 tests [0;32mOK[0m
test_datatypes.R.............. 4 tests [0;32mOK[0m
test_datatypes.R.............. 5 tests [0;32mOK[0m
test_datatypes.R.............. 6 tests [0;32mOK[0m
test_datatypes.R.............. 7 tests [0;32mOK[0m
test_datatypes.R.............. 8 tests [0;32mOK[0m
test_datatypes.R.............. 9 tests [0;32mOK[0m
test_datatypes.R.............. 10 tests [0;32mOK[0m
test_datatypes.R.............. 11 tests [0;32mOK[0m
test_datatypes.R.............. 12 tests [0;32mOK[0m
test_datatypes.R.............. 13 tests [0;32mOK[0m
test_datatypes.R.............. 14 tests [0;32mOK[0m
test_datatypes.R.............. 15 tests [0;32mOK[0m
test_datatypes.R.............. 16 tests [0;32mOK[0m [0;36m6ms[0m
test_decompression.R.......... 0 tests
test_decompression.R.......... 12 tests [0;32mOK[0m [0;36m21ms[0m
test_fill_values.R............ 0 tests
test_fill_values.R............ 0 tests
test_fill_values.R............ 10 tests [0;32mOK[0m [0;36m15ms[0m
test_float16.R................ 0 tests
test_float16.R................ 0 tests
test_float16.R................ 0 tests
test_float16.R................ 1 tests [0;32mOK[0m
test_float16.R................ 2 tests [0;32mOK[0m
test_float16.R................ 3 tests [0;32mOK[0m
test_float16.R................ 4 tests [0;32mOK[0m
test_float16.R................ 5 tests [0;32mOK[0m
test_float16.R................ 6 tests [0;32mOK[0m
test_float16.R................ 7 tests [0;32mOK[0m
test_float16.R................ 8 tests [0;32mOK[0m
test_float16.R................ 9 tests [0;32mOK[0m [0;36m18ms[0m
test_float32.R................ 0 tests
test_float32.R................ 0 tests
test_float32.R................ 0 tests
test_float32.R................ 1 tests [0;32mOK[0m
test_float32.R................ 2 tests [0;32mOK[0m
test_float32.R................ 3 tests [0;32mOK[0m
test_float32.R................ 4 tests [0;32mOK[0m
test_float32.R................ 5 tests [0;32mOK[0m
test_float32.R................ 6 tests [0;32mOK[0m
test_float32.R................ 7 tests [0;32mOK[0m [0;36m18ms[0m
test_float64.R................ 0 tests
test_float64.R................ 0 tests
test_float64.R................ 0 tests
test_float64.R................ 1 tests [0;32mOK[0m
test_float64.R................ 2 tests [0;32mOK[0m
test_float64.R................ 3 tests [0;32mOK[0m
test_float64.R................ 4 tests [0;32mOK[0m
test_float64.R................ 5 tests [0;32mOK[0m
test_float64.R................ 6 tests [0;32mOK[0m
test_float64.R................ 7 tests [0;32mOK[0m [0;36m18ms[0m
test_int16.R.................. 0 tests
test_int16.R.................. 0 tests
test_int16.R.................. 0 tests
test_int16.R.................. 1 tests [0;32mOK[0m
test_int16.R.................. 2 tests [0;32mOK[0m
test_int16.R.................. 3 tests [0;32mOK[0m
test_int16.R.................. 4 tests [0;32mOK[0m
test_int16.R.................. 5 tests [0;32mOK[0m
test_int16.R.................. 6 tests [0;32mOK[0m
test_int16.R.................. 7 tests [0;32mOK[0m [0;36m17ms[0m
test_int32.R.................. 0 tests
test_int32.R.................. 0 tests
test_int32.R.................. 0 tests
test_int32.R.................. 1 tests [0;32mOK[0m
test_int32.R.................. 2 tests [0;32mOK[0m
test_int32.R.................. 3 tests [0;32mOK[0m
test_int32.R.................. 4 tests [0;32mOK[0m
test_int32.R.................. 5 tests [0;32mOK[0m
test_int32.R.................. 6 tests [0;32mOK[0m
test_int32.R.................. 7 tests [0;32mOK[0m [0;36m19ms[0m
test_int64.R.................. 0 tests
test_int64.R.................. 0 tests
test_int64.R.................. 0 tests
test_int64.R.................. 1 tests [0;32mOK[0m
test_int64.R.................. 2 tests [0;32mOK[0m
test_int64.R.................. 3 tests [0;32mOK[0m
test_int64.R.................. 4 tests [0;32mOK[0m
test_int64.R.................. 5 tests [0;32mOK[0m
test_int64.R.................. 6 tests [0;32mOK[0m
test_int64.R.................. 7 tests [0;32mOK[0m
test_int64.R.................. 8 tests [0;32mOK[0m
test_int64.R.................. 9 tests [0;32mOK[0m
test_int64.R.................. 10 tests [0;32mOK[0m
test_int64.R.................. 11 tests [0;32mOK[0m
test_int64.R.................. 12 tests [0;32mOK[0m
test_int64.R.................. 13 tests [0;32mOK[0m
test_int64.R.................. 14 tests [0;32mOK[0m
test_int64.R.................. 15 tests [0;32mOK[0m [0;36m30ms[0m
test_int8.R................... 0 tests
test_int8.R................... 0 tests
test_int8.R................... 0 tests
test_int8.R................... 1 tests [0;32mOK[0m
test_int8.R................... 2 tests [0;32mOK[0m
test_int8.R................... 3 tests [0;32mOK[0m
test_int8.R................... 4 tests [0;32mOK[0m
test_int8.R................... 5 tests [0;32mOK[0m
test_int8.R................... 6 tests [0;32mOK[0m
test_int8.R................... 7 tests [0;32mOK[0m [0;36m17ms[0m
test_normalize_path.R......... 0 tests
test_normalize_path.R......... 0 tests
test_normalize_path.R......... 3 tests [0;32mOK[0m [0;36m3ms[0m
test_read_metadata.R.......... 0 tests
test_read_metadata.R.......... 0 tests
test_read_metadata.R.......... 1 tests [0;32mOK[0m
test_read_metadata.R.......... 2 tests [0;32mOK[0m
test_read_metadata.R.......... 3 tests [0;32mOK[0m [0;36m10ms[0m
test_roundtrip.R.............. 0 tests
test_roundtrip.R.............. 1 tests [0;32mOK[0m
test_roundtrip.R.............. 2 tests [0;32mOK[0m
test_roundtrip.R.............. 3 tests [0;32mOK[0m
test_roundtrip.R.............. 3 tests [0;32mOK[0m
test_roundtrip.R.............. 3 tests [0;32mOK[0m
test_roundtrip.R.............. 4 tests [0;32mOK[0m
test_roundtrip.R.............. 5 tests [0;32mOK[0m
test_roundtrip.R.............. 5 tests [0;32mOK[0m
test_roundtrip.R.............. 6 tests [0;32mOK[0m
test_roundtrip.R.............. 7 tests [0;32mOK[0m
test_roundtrip.R.............. 7 tests [0;32mOK[0m
test_roundtrip.R.............. 8 tests [0;32mOK[0m
test_roundtrip.R.............. 9 tests [0;32mOK[0m
test_roundtrip.R.............. 9 tests [0;32mOK[0m
test_roundtrip.R.............. 10 tests [0;32mOK[0m
test_roundtrip.R.............. 11 tests [0;32mOK[0m
test_roundtrip.R.............. 11 tests [0;32mOK[0m
test_roundtrip.R.............. 12 tests [0;32mOK[0m
test_roundtrip.R.............. 13 tests [0;32mOK[0m
test_roundtrip.R.............. 13 tests [0;32mOK[0m
test_roundtrip.R.............. 14 tests [0;32mOK[0m
test_roundtrip.R.............. 15 tests [0;32mOK[0m
test_roundtrip.R.............. 15 tests [0;32mOK[0m
test_roundtrip.R.............. 16 tests [0;32mOK[0m
test_roundtrip.R.............. 17 tests [0;32mOK[0m
test_roundtrip.R.............. 17 tests [0;32mOK[0m
test_roundtrip.R.............. 18 tests [0;32mOK[0m
test_roundtrip.R.............. 19 tests [0;32mOK[0m
test_roundtrip.R.............. 19 tests [0;32mOK[0m
test_roundtrip.R.............. 20 tests [0;32mOK[0m
test_roundtrip.R.............. 21 tests [0;32mOK[0m [0;34m2.1s[0m
test_s3.R..................... 0 tests
test_s3.R..................... 0 tests Loading required package: mockery
test_s3.R..................... 1 tests [0;32mOK[0m [0;34m0.1s[0m
test_string.R................. 0 tests
test_string.R................. 0 tests
test_string.R................. 0 tests
test_string.R................. 1 tests [0;32mOK[0m
test_string.R................. 2 tests [0;32mOK[0m
test_string.R................. 3 tests [0;32mOK[0m
test_string.R................. 4 tests [0;32mOK[0m
test_string.R................. 5 tests [0;32mOK[0m
test_string.R................. 6 tests [0;32mOK[0m
test_string.R................. 7 tests [0;32mOK[0m
test_string.R................. 7 tests [0;32mOK[0m
test_string.R................. 8 tests [0;32mOK[0m
test_string.R................. 9 tests [0;32mOK[0m
test_string.R................. 9 tests [0;32mOK[0m
test_string.R................. 10 tests [0;32mOK[0m
test_string.R................. 11 tests [0;32mOK[0m
test_string.R................. 11 tests [0;32mOK[0m
test_string.R................. 11 tests [0;32mOK[0m
test_string.R................. 12 tests [0;32mOK[0m
test_string.R................. 13 tests [0;32mOK[0m
test_string.R................. 14 tests [0;32mOK[0m
test_string.R................. 14 tests [0;32mOK[0m
test_string.R................. 15 tests [0;32mOK[0m
test_string.R................. 16 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 17 tests [0;32mOK[0m
test_string.R................. 18 tests [0;32mOK[0m [0;34m0.4s[0m
test_uint16.R................. 0 tests
test_uint16.R................. 0 tests
test_uint16.R................. 1 tests [0;32mOK[0m
test_uint16.R................. 2 tests [0;32mOK[0m
test_uint16.R................. 3 tests [0;32mOK[0m
test_uint16.R................. 4 tests [0;32mOK[0m
test_uint16.R................. 5 tests [0;32mOK[0m [0;36m14ms[0m
test_uint32.R................. 0 tests
test_uint32.R................. 0 tests
test_uint32.R................. 0 tests
test_uint32.R................. 1 tests [0;32mOK[0m
test_uint32.R................. 2 tests [0;32mOK[0m
test_uint32.R................. 3 tests [0;32mOK[0m
test_uint32.R................. 4 tests [0;32mOK[0m
test_uint32.R................. 5 tests [0;32mOK[0m
test_uint32.R................. 6 tests [0;32mOK[0m
test_uint32.R................. 7 tests [0;32mOK[0m
test_uint32.R................. 8 tests [0;32mOK[0m
test_uint32.R................. 9 tests [0;32mOK[0m
test_uint32.R................. 10 tests [0;32mOK[0m
test_uint32.R................. 11 tests [0;32mOK[0m [0;36m43ms[0m
test_uint64.R................. 0 tests
test_uint64.R................. 0 tests
test_uint64.R................. 1 tests [0;32mOK[0m
test_uint64.R................. 2 tests [0;32mOK[0m
test_uint64.R................. 3 tests [0;32mOK[0m
test_uint64.R................. 4 tests [0;32mOK[0m
test_uint64.R................. 5 tests [0;32mOK[0m
test_uint64.R................. 6 tests [0;32mOK[0m
test_uint64.R................. 7 tests [0;32mOK[0m [0;36m19ms[0m
test_uint8.R.................. 0 tests
test_uint8.R.................. 0 tests
test_uint8.R.................. 1 tests [0;32mOK[0m
test_uint8.R.................. 2 tests [0;32mOK[0m
test_uint8.R.................. 3 tests [0;32mOK[0m
test_uint8.R.................. 4 tests [0;32mOK[0m
test_uint8.R.................. 5 tests [0;32mOK[0m [0;36m15ms[0m
test_update_zarr.R............ 0 tests
test_update_zarr.R............ 0 tests
test_update_zarr.R............ 0 tests
test_update_zarr.R............ 1 tests [0;32mOK[0m
test_update_zarr.R............ 2 tests [0;32mOK[0m
test_update_zarr.R............ 3 tests [0;32mOK[0m
test_update_zarr.R............ 3 tests [0;32mOK[0m
test_update_zarr.R............ 4 tests [0;32mOK[0m
test_update_zarr.R............ 5 tests [0;32mOK[0m
test_update_zarr.R............ 6 tests [0;32mOK[0m [0;36m40ms[0m
test_url_parsing.R............ 0 tests
test_url_parsing.R............ 10 tests [0;32mOK[0m
test_url_parsing.R............ 15 tests [0;32mOK[0m
test_url_parsing.R............ 16 tests [0;32mOK[0m
test_url_parsing.R............ 17 tests [0;32mOK[0m
test_url_parsing.R............ 18 tests [0;32mOK[0m [0;36m9ms[0m
test_utils.R.................. 1 tests [0;32mOK[0m
test_utils.R.................. 2 tests [0;32mOK[0m
test_utils.R.................. 3 tests [0;32mOK[0m [0;36m2ms[0m
All ok, 204 results (3.1s)
>
> proc.time()
user system elapsed
2.79 1.01 4.25
Rarr.Rcheck/Rarr-Ex.timings
| name | user | system | elapsed | |
| compressors | 0.31 | 0.16 | 0.53 | |
| create_empty_zarr_array | 0.02 | 0.00 | 0.01 | |
| read_zarr_array | 0.05 | 0.01 | 0.06 | |
| update_zarr_array | 0.00 | 0.00 | 0.03 | |
| write_zarr_array | 0.00 | 0.00 | 0.02 | |
| zarr_overview | 0.14 | 0.06 | 1.12 | |