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This page was generated on 2023-10-20 09:38:02 -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 766/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.36.1  (landing page)
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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

INSTALL results for gdsfmt on kjohnson2


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.

raw results


Summary

Package: gdsfmt
Version: 1.36.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gdsfmt
StartedAt: 2023-10-15 15:02:28 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 15:07:57 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 329.1 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gdsfmt
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/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)