Xiuwen Zheng
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/gdsfmt |
| git_branch: RELEASE_3_17 |
| git_last_commit: 02524c5 |
| git_last_commit_date: 2023-07-03 21:15:05 -0400 (Mon, 03 Jul 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 766/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gdsfmt 1.36.1 (landing page) Xiuwen Zheng
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the gdsfmt 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. |
| Package: gdsfmt |
| Version: 1.36.1 |
| Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.36.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir |
| StartedAt: 2023-10-19 13:32:14 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 13:39:58 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 464.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: gdsfmt_1.36.1.tgz |
| PackageFileSize: 1.697 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.36.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gdsfmt.buildbin-libdir gdsfmt_1.36.1.tar.gz' >>>>>>> * installing *source* package ‘gdsfmt’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gdsfmt.cpp -o gdsfmt.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c digest.cpp -o digest.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/compress.c -o ZLIB/compress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/infback.c -o ZLIB/infback.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/trees.c -o ZLIB/trees.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4.c -o LZ4/lz4.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4hc.c -o LZ4/lz4hc.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/lz4frame.c -o LZ4/lz4frame.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LZ4/xxhash.c -o LZ4/xxhash.o cd XZ && tar -xzf xz-5.2.9.tar.gz cd XZ/xz-5.2.9 && \ ./configure CC="clang -arch arm64" CPP="clang -arch arm64 -E" CXX="clang++ -arch arm64 -std=gnu++17" CXXCPP="" --build="" \ --with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null cd XZ/xz-5.2.9/src/liblzma && make Making all in api make[2]: Nothing to be done for `all'. CC liblzma_la-tuklib_physmem.lo CC liblzma_la-tuklib_cpucores.lo CC liblzma_la-common.lo CC liblzma_la-block_util.lo CC liblzma_la-easy_preset.lo CC liblzma_la-filter_common.lo CC liblzma_la-hardware_physmem.lo CC liblzma_la-index.lo CC liblzma_la-stream_flags_common.lo CC liblzma_la-vli_size.lo CC liblzma_la-hardware_cputhreads.lo CC liblzma_la-alone_encoder.lo CC liblzma_la-block_buffer_encoder.lo CC liblzma_la-block_encoder.lo CC liblzma_la-block_header_encoder.lo CC liblzma_la-easy_buffer_encoder.lo CC liblzma_la-easy_encoder.lo CC liblzma_la-easy_encoder_memusage.lo CC liblzma_la-filter_buffer_encoder.lo CC liblzma_la-filter_encoder.lo CC liblzma_la-filter_flags_encoder.lo CC liblzma_la-index_encoder.lo CC liblzma_la-stream_buffer_encoder.lo CC liblzma_la-stream_encoder.lo CC liblzma_la-stream_flags_encoder.lo CC liblzma_la-vli_encoder.lo CC liblzma_la-outqueue.lo CC liblzma_la-stream_encoder_mt.lo CC liblzma_la-alone_decoder.lo CC liblzma_la-auto_decoder.lo CC liblzma_la-block_buffer_decoder.lo CC liblzma_la-block_decoder.lo CC liblzma_la-block_header_decoder.lo CC liblzma_la-easy_decoder_memusage.lo CC liblzma_la-filter_buffer_decoder.lo CC liblzma_la-filter_decoder.lo CC liblzma_la-filter_flags_decoder.lo CC liblzma_la-index_decoder.lo CC liblzma_la-index_hash.lo CC liblzma_la-stream_buffer_decoder.lo CC liblzma_la-stream_decoder.lo CC liblzma_la-stream_flags_decoder.lo CC liblzma_la-vli_decoder.lo CC liblzma_la-check.lo CC liblzma_la-crc32_table.lo CC liblzma_la-crc32_fast.lo CC liblzma_la-crc64_table.lo CC liblzma_la-crc64_fast.lo CC liblzma_la-sha256.lo CC liblzma_la-lz_encoder.lo CC liblzma_la-lz_encoder_mf.lo CC liblzma_la-lz_decoder.lo CC liblzma_la-lzma_encoder_presets.lo CC liblzma_la-lzma_encoder.lo CC liblzma_la-lzma_encoder_optimum_fast.lo CC liblzma_la-lzma_encoder_optimum_normal.lo CC liblzma_la-fastpos_table.lo CC liblzma_la-lzma_decoder.lo CC liblzma_la-lzma2_encoder.lo CC liblzma_la-lzma2_decoder.lo CC liblzma_la-price_table.lo CC liblzma_la-delta_common.lo CC liblzma_la-delta_encoder.lo CC liblzma_la-delta_decoder.lo CC liblzma_la-simple_coder.lo CC liblzma_la-simple_encoder.lo CC liblzma_la-simple_decoder.lo CC liblzma_la-x86.lo CC liblzma_la-powerpc.lo CC liblzma_la-ia64.lo CC liblzma_la-arm.lo CC liblzma_la-armthumb.lo CC liblzma_la-sparc.lo CCLD liblzma.la PC liblzma.pc cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a . rm -rf XZ/xz-5.2.9/dos rm -rf XZ/xz-5.2.9/po clang++ -arch arm64 -std=gnu++17 -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 gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gdsfmt.buildbin-libdir/00LOCK-gdsfmt/00new/gdsfmt/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 (gdsfmt) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so >>>>>>> >>>>>>> Paths before fix: gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so: gdsfmt.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) >>>>>>> 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" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so" >>>>>>> Paths after fix: gdsfmt.buildbin-libdir/gdsfmt/libs/gdsfmt.so: gdsfmt.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /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/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)