Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1631/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rarr 1.0.3  (landing page)
Mike Smith
Snapshot Date: 2023-10-15 14:00:07 -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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for Rarr on kjohnson2


To the developers/maintainers of the Rarr package:
- 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: rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.0.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rarr.buildbin-libdir
StartedAt: 2023-10-19 16:12:28 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 16:14:32 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 123.9 seconds
RetCode: 0
Status:   OK  
PackageFile: Rarr_1.0.3.tgz
PackageFileSize: 1.186 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rarr.buildbin-libdir && mkdir Rarr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rarr_1.0.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rarr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rarr.buildbin-libdir Rarr_1.0.3.tar.gz'
>>>>>>> 

* installing *source* package ‘Rarr’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
x86_CPU=false
checking for gcc... clang -arch arm64
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 clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to enable C11 features... none needed
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
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/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:569:13: 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/zstd-1.4.5
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -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 -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 -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 -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 -I. -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
compress/zstd_compress_superblock.c:412:12: warning: variable 'litLengthSum' set but not used [-Wunused-but-set-variable]
    size_t litLengthSum = 0;
           ^
1 warning generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -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 -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 -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 -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 -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 -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 -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 -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 -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 -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
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-1.4.5   -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-1.4.5   -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-1.4.5   -DUSING_R   -c shuffle.c
shuffle.c:318:22: 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-1.4.5   -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-1.4.5   -DUSING_R -c blosc.c
blosc.c:744:11: warning: variable 'ctbytes' set but not used [-Wunused-but-set-variable]
  int32_t ctbytes = 0;           /* number of compressed bytes in block */
          ^
blosc.c:305:12: 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-1.4.5   -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 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
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)