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This page was generated on 2026-03-23 11:35 -0400 (Mon, 23 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4868
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" 4548
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 816/2368HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.47.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2026-03-22 13:40 -0400 (Sun, 22 Mar 2026)
git_url: https://git.bioconductor.org/packages/gdsfmt
git_branch: devel
git_last_commit: 650aa25
git_last_commit_date: 2025-10-29 10:23:33 -0400 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    ERROR  
See other builds for gdsfmt in R Universe.

BUILD BIN results for gdsfmt on kjohnson3

To the developers/maintainers of the gdsfmt package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gdsfmt.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.

raw results


Summary

Package: gdsfmt
Version: 1.47.0
Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R gdsfmt.buildbin-libdir
StartedAt: 2026-03-22 22:51:25 -0400 (Sun, 22 Mar 2026)
EndedAt: 2026-03-22 22:52:50 -0400 (Sun, 22 Mar 2026)
EllapsedTime: 84.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.47.0.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_1.47.0.tar.gz'
>>>>>>> 

* installing *source* package ‘gdsfmt’ ...
** this is package ‘gdsfmt’ version ‘1.47.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang++ -arch arm64 -std=gnu++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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 -std=gnu23 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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++20 -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 -std=gnu23 -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
In file included from ZLIB/adler32.c:8:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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
In file included from ZLIB/crc32.c:30:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/deflate.c:52:
In file included from ZLIB/deflate.h:16:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/infback.c:13:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/inffast.c:6:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/inflate.c:83:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/inftrees.c:6:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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
In file included from ZLIB/trees.c:37:
In file included from ZLIB/deflate.h:16:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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
In file included from ZLIB/zutil.c:8:
ZLIB/zutil.h:170:11: warning: 'OS_CODE' macro redefined [-Wmacro-redefined]
  170 | #  define OS_CODE 19
      |           ^
ZLIB/zutil.h:141:11: note: previous definition is here
  141 | #  define OS_CODE  7
      |           ^
1 warning generated.
clang -arch arm64 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23 -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 -std=gnu23" CPP="clang -arch arm64 -std=gnu23 -E" CXX="clang++ -arch arm64 -std=gnu++20" 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++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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
installing to /Users/biocbuild/bbs-3.23-bioc/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 1356.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)

>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!