Hugo Gruson
| Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/Rarr |
| git_branch: devel |
| git_last_commit: 5ad8984 |
| git_last_commit_date: 2026-03-16 10:57:16 -0400 (Mon, 16 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-21 11:35 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 1721/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rarr 1.11.31 (landing page) Hugo Gruson
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for Rarr in R Universe. | ||||||||||||||
|
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: 1.11.31 |
| Command: rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.11.31.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rarr.buildbin-libdir |
| StartedAt: 2026-03-21 02:41:32 -0400 (Sat, 21 Mar 2026) |
| EndedAt: 2026-03-21 02:41:57 -0400 (Sat, 21 Mar 2026) |
| EllapsedTime: 25.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.11.31.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rarr.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rarr.buildbin-libdir Rarr_1.11.31.tar.gz'
>>>>>>>
* installing *source* package ‘Rarr’ ...
** this is package ‘Rarr’ version ‘1.11.31’
** 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-1.21.6/Makefile
config.status: creating src/compression_tools/blosc/Makefile
config.status: creating src/compression_tools/blosc/lib/snappy-1.2.2/Makefile
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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-1.5.7
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -c -o compress/zstd_preSplit.o compress/zstd_preSplit.c
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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/zstd_preSplit.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-1.2.2
clang++ -arch arm64 -std=gnu++20 -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:1957:23: warning: private field 'output_iov_' is not used [-Wunused-private-field]
1957 | const struct iovec* output_iov_;
| ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -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++20 -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++20 -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/lz4-1.10.0
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -DNLZ4_DEBUG -c lz4.c
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -DNLZ4_DEBUG -c lz4hc.c
make -C lib/blosc-1.21.6 all
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c bitshuffle-generic.c
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c shuffle-generic.c
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c shuffle.c
shuffle.c:297:22: warning: unused variable 'cpu_features' [-Wunused-variable]
297 | 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]
32 | static void shuffle_generic_inline(const size_t type_size,
| ^~~~~~~~~~~~~~~~~~~~~~
./shuffle-generic.h:61:13: warning: unused function 'unshuffle_generic_inline' [-Wunused-function]
61 | static void unshuffle_generic_inline(const size_t type_size,
| ^~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c blosclz.c
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c blosc.c
blosc.c:741:11: warning: variable 'ctbytes' set but not used [-Wunused-but-set-variable]
741 | int32_t ctbytes = 0; /* number of compressed bytes in block */
| ^
blosc.c:302:12: warning: unused function 'compname_to_clibcode' [-Wunused-function]
302 | static int compname_to_clibcode(const char *compname)
| ^~~~~~~~~~~~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I/Library/Frameworks/R.framework/Resources/include -I../lz4-1.10.0 -I../snappy-1.2.2 -I../../../zstd-1.5.7 -DUSING_R -c fastcopy.c
fastcopy.c:70:30: warning: unused function 'copy_5_bytes' [-Wunused-function]
70 | static inline unsigned char *copy_5_bytes(unsigned char *out, const unsigned char *from) {
| ^~~~~~~~~~~~
fastcopy.c:75:30: warning: unused function 'copy_6_bytes' [-Wunused-function]
75 | static inline unsigned char *copy_6_bytes(unsigned char *out, const unsigned char *from) {
| ^~~~~~~~~~~~
fastcopy.c:80:30: warning: unused function 'copy_7_bytes' [-Wunused-function]
80 | 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-1.21.6/blosc.o lib/blosc-1.21.6/bitshuffle-generic.o lib/blosc-1.21.6/blosclz.o lib/blosc-1.21.6/shuffle.o lib/blosc-1.21.6/fastcopy.o lib/blosc-1.21.6/shuffle-generic.o lib/snappy-1.2.2/snappy.o lib/snappy-1.2.2/snappy-c.o lib/snappy-1.2.2/snappy-sinksource.o lib/snappy-1.2.2/snappy-stubs-internal.o lib/lz4-1.10.0/lz4.o lib/lz4-1.10.0/lz4hc.o
ranlib libblosc.a
clang -arch arm64 -std=gnu23 -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-1.5.7/libzstd.a -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/Rarr.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Rarr.buildbin-libdir/Rarr/libs/Rarr.so
>>>>>>>
>>>>>>> Paths before fix:
Rarr.buildbin-libdir/Rarr/libs/Rarr.so:
Rarr.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!