BioC 3.5: BUILD BIN report for gdsfmt on veracruz2

Package: gdsfmt

Version: 1.12.0

Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gdsfmt.buildbin-libdir

StartedAt: 2017-08-16 10:15:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 10:17:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 155.7 seconds

RetCode: 0

Status:  OK

PackageFile: gdsfmt_1.12.0.tgz

PackageFileSize: 1.609 MiB

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### Running command:
###
###   rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gdsfmt.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gdsfmt.buildbin-libdir gdsfmt_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘gdsfmt’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_CoreArray.cpp -o R_CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c gdsfmt.cpp -o gdsfmt.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c digest.cpp -o digest.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/adler32.c -o ZLIB/adler32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/compress.c -o ZLIB/compress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/crc32.c -o ZLIB/crc32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/deflate.c -o ZLIB/deflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/infback.c -o ZLIB/infback.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inffast.c -o ZLIB/inffast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inflate.c -o ZLIB/inflate.o
ZLIB/inflate.c:1507:61: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
    if (strm == Z_NULL || strm->state == Z_NULL) return -1L << 16;
                                                        ˜˜˜ ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/trees.c -o ZLIB/trees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c ZLIB/zutil.c -o ZLIB/zutil.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4.c -o LZ4/lz4.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include   -fPIC  -Wall -g -O2  -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.3.tar.gz
cd XZ/xz-5.2.3 && \
		./configure CC="clang" CPP="clang -E" CXX="clang++ " CXXCPP="clang++  -E" --build="" --with-pic --enable-silent-rules --quiet > /dev/null
cd XZ/xz-5.2.3/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
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
  PC       liblzma.pc
cp XZ/xz-5.2.3/src/liblzma/.libs/liblzma.a .
rm -rf XZ/xz-5.2.3/dos
rm -rf XZ/xz-5.2.3/po
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/dSerial.o CoreArray/dStream.o CoreArray/dStruct.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-3.5-bioc/meat/gdsfmt.buildbin-libdir/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
* DONE (gdsfmt)


>>>>>>> 
>>>>>>> FIXING LINKS FOR gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"