Mike Smith
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/Rarr |
| git_branch: devel |
| git_last_commit: 8f1c9da |
| git_last_commit_date: 2024-11-25 11:19:30 -0500 (Mon, 25 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1652/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rarr 1.7.1 (landing page) Mike Smith
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.7.1 |
| Command: rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.7.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rarr.buildbin-libdir |
| StartedAt: 2024-12-23 22:40:10 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 22:40:35 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 24.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rarr_1.7.1.tgz |
| PackageFileSize: 1.423 MiB |
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###
### Running command:
###
### rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.7.1.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_1.7.1.tar.gz'
>>>>>>>
* 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-1500.1.0.2.5)’
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 /Users/biocbuild/bbs-3.21-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/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rarr.buildbin-libdir/Rarr/libs/Rarr.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "Rarr.buildbin-libdir/Rarr/libs/Rarr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "Rarr.buildbin-libdir/Rarr/libs/Rarr.so"
>>>>>>> Paths after 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/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)