Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:35:39 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1631/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rarr 1.0.3  (landing page)
Mike Smith
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Rarr
git_branch: RELEASE_3_17
git_last_commit: 4d4228f
git_last_commit_date: 2023-09-21 05:58:32 -0400 (Thu, 21 Sep 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for Rarr on nebbiolo1


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: 1.0.3
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Rarr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Rarr_1.0.3.tar.gz
StartedAt: 2023-10-16 00:13:55 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:14:37 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 42.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Rarr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Rarr.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings Rarr_1.0.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Rarr.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Rarr/DESCRIPTION’ ... OK
* this is package ‘Rarr’ version ‘1.0.3’
* 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/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/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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rarr’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 ... 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
* 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 ...
  ‘Rarr.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/Rarr.Rcheck/00check.log’
for details.



Installation output

Rarr.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rarr
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘Rarr’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
x86_CPU=true
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... yes
checking for gcc __builtin_cpu_init function... (cached) true
checking for x86 sse2 instruction support... yes
checking for x86 avx2 instruction support... yes
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
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c Rarr.c -o Rarr.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c bit64_conversion.c -o bit64_conversion.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c compress.c -o compress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c decompress.c -o decompress.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c float16_conversion.c -o float16_conversion.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fpic  -g -O2  -Wall -c type_conversion.c -o type_conversion.o
make -C compression_tools/blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -DUSING_R -c snappy.cc
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::Append(const char*, size_t)’:
snappy.cc:1012:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1012 |         if (curr_iov_index_ + 1 >= output_iov_count_) {
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)’:
snappy.cc:1094:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1094 |           if (curr_iov_index_ + 1 >= output_iov_count_) {
      |               ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: At global scope:
snappy.cc:569:13: warning: ‘void snappy::ComputeTable()’ defined but not used [-Wunused-function]
  569 | static void ComputeTable() {
      |             ^~~~~~~~~~~~
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -DUSING_R -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -DUSING_R -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -DUSING_R -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-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-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
gcc -g -O2 -Wall -fpic -DNLZ4_DEBUG -c lz4.c
gcc -g -O2 -Wall -fpic -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
make -C lib/zstd-1.4.5
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c bitshuffle-avx2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c shuffle-avx2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c bitshuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c shuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c bitshuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c shuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_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,
      |             ^~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c blosclz.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -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)
      |            ^~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Wall -fpic -I/usr/local/include -I/home/biocbuild/bbs-3.17-bioc/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DUSING_R -c fastcopy.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-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/bitshuffle-avx2.o lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-avx2.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 '/home/biocbuild/bbs-3.17-bioc/meat/Rarr/src/compression_tools/blosc'
gcc -shared -L/home/biocbuild/bbs-3.17-bioc/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 -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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)

Tests output

Rarr.Rcheck/tests/tinytest.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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_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 60ms

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 5ms

test_decompression.R..........    0 tests    
test_decompression.R..........   12 tests OK 13ms

test_fill_values.R............    0 tests    
test_fill_values.R............    0 tests    
test_fill_values.R............   10 tests OK 14ms

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 10ms

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 59ms

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 11ms

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 10ms

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 11ms

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 20ms

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 12ms

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

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 0.5s

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 9ms

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 6ms

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 14ms

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 8ms

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 6ms

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 13ms

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
All ok, 185 results (0.8s)
> 
> proc.time()
   user  system elapsed 
  1.262   0.160   1.419 

Example timings

Rarr.Rcheck/Rarr-Ex.timings

nameusersystemelapsed
compressors0.1810.0160.197
create_empty_zarr_array0.0000.0020.002
read_zarr_array0.0170.0270.045
update_zarr_array0.0070.0000.006
write_zarr_array0.0050.0000.004
zarr_overview0.2450.0243.566