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BioC 3.5: INSTALL report for gdsfmt on oaxaca

This page was generated on 2017-03-04 16:48:58 -0500 (Sat, 04 Mar 2017).

Package 482/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.11.3
Xiuwen Zheng
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gdsfmt
Last Changed Rev: 125749 / Revision: 127142
Last Changed Date: 2017-01-06 15:22:06 -0500 (Fri, 06 Jan 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64 [ OK ] OK  OK  OK 

Summary

Package: gdsfmt
Version: 1.11.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gdsfmt
StartedAt: 2017-03-03 15:08:16 -0800 (Fri, 03 Mar 2017)
EndedAt: 2017-03-03 15:10:08 -0800 (Fri, 03 Mar 2017)
EllapsedTime: 112.3 seconds
RetCode: 0
Status:  OK 

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘gdsfmt’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c R_CoreArray.cpp -o R_CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c gdsfmt.cpp -o gdsfmt.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c digest.cpp -o digest.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/adler32.c -o ZLIB/adler32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/compress.c -o ZLIB/compress.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/crc32.c -o ZLIB/crc32.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/deflate.c -o ZLIB/deflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/infback.c -o ZLIB/infback.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/inffast.c -o ZLIB/inffast.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/inflate.c -o ZLIB/inflate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/trees.c -o ZLIB/trees.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ZLIB/zutil.c -o ZLIB/zutil.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LZ4/lz4.c -o LZ4/lz4.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && tar -xzf xz-5.2.2.tar.gz
cd XZ/xz-5.2.2 && \
		./configure CC="clang" CPP="clang -E" CXX="clang++ " CXXCPP="clang++  -E" --build="" --with-pic --enable-silent-rules --quiet > /dev/null
cd XZ/xz-5.2.2/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-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-hardware_cputhreads.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-lz_encoder.lo
  CC       liblzma_la-lz_encoder_mf.lo
  CC       liblzma_la-lz_decoder.lo
  CC       liblzma_la-lzma_encoder.lo
  CC       liblzma_la-lzma_encoder_presets.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: warning: argument unused during compilation: '-pthread'
clang: warning: argument unused during compilation: '-pthread'
  PC       liblzma.pc
cp XZ/xz-5.2.2/src/liblzma/.libs/liblzma.a .
rm -rf XZ/xz-5.2.2/dos
rm -rf XZ/xz-5.2.2/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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/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)