Xiuwen Zheng
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/gdsfmt |
| Branch: RELEASE_3_6 |
| Last Commit: 1574364 |
| Last Changed Date: 2017-12-16 19:13:23 -0400 (Sat, 16 Dec 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:40:10 -0400 (Thu, 12 Apr 2018).
| Package 525/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gdsfmt 1.14.1 Xiuwen Zheng
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: gdsfmt |
| Version: 1.14.1 |
| Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.14.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gdsfmt.buildbin-libdir |
| StartedAt: 2018-04-12 11:31:10 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 11:34:03 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 172.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: gdsfmt_1.14.1.tgz |
| PackageFileSize: 1.594 MiB |
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### Running command:
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### rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.14.1.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_1.14.1.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-3.6-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"