gdsfmt

Package: gdsfmt
Type: Package
Title: R Interface to CoreArray Genomic Data Structure (GDS) Files
Version: 1.8.3
Date: 2016-06-12
Depends: R (>= 2.15.0)
Imports: methods
Suggests: parallel, digest, crayon, RUnit, knitr, BiocGenerics
Author: Xiuwen Zheng [aut, cre], Stephanie Gogarten [ctb], Jean-loup
Gailly and Mark Adler [ctb] (for the included zlib sources),
Yann Collet [ctb] (for the included LZ4 sources),
xz contributors (for the included liblzma sources)
Maintainer: Xiuwen Zheng <zhengx@u.washington.edu>
Description: This package provides a high-level R interface to
CoreArray Genomic Data Structure (GDS) data files, which are
portable across platforms with hierarchical structure to
store multiple scalable array-oriented data sets with metadata
information. It is suited for large-scale datasets, especially
for data which are much larger than the available random-access
memory. The gdsfmt package offers the efficient operations
specifically designed for integers of less than 8 bits, since
a single genetic/genomic variant, like single-nucleotide
polymorphism (SNP), usually occupies fewer bits than a byte.
Data compression and decompression are available with relatively
efficient random access. It is also allowed to read a GDS
file in parallel with multiple R processes supported by the
package parallel.
License: LGPL-3
Copyright: This package includes the sources of CoreArray C++ library
written by Xiuwen Zheng (LGPL-3), zlib written by Jean-loup
Gailly and Mark Adler (zlib license), LZ4 written by Yann
Collet (simplified BSD), and liblzma written by Lasse Collin
and other xz contributors (public domain).
VignetteBuilder: knitr
ByteCompile: TRUE
BugReports: http://github.com/zhengxwen/gdsfmt/issues
URL: http://corearray.sourceforge.net/
http://github.com/zhengxwen/gdsfmt
biocViews: Software, Infrastructure, DataImport
NeedsCompilation: yes
Packaged: 2016-06-14 05:01:07 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'gdsfmt' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c R_CoreArray.cpp -o R_CoreArray.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c gdsfmt.cpp -o gdsfmt.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c digest.cpp -o digest.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/adler32.c -o ZLIB/adler32.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/compress.c -o ZLIB/compress.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/crc32.c -o ZLIB/crc32.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/deflate.c -o ZLIB/deflate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/infback.c -o ZLIB/infback.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/inffast.c -o ZLIB/inffast.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/inflate.c -o ZLIB/inflate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/trees.c -o ZLIB/trees.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c ZLIB/zutil.c -o ZLIB/zutil.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c LZ4/lz4.c -o LZ4/lz4.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -g -O2  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fpic  -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="gcc" CPP="gcc -E" CXX="g++" CXXCPP="g++ -E" --build="" --with-pic --enable-silent-rules --quiet > /dev/null
cd XZ/xz-5.2.2/src/liblzma && make
make[1]: Entering directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma'
Making all in api
make[2]: Entering directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma/api'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma/api'
make[2]: Entering directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma'
  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-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.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
ar: `u' modifier ignored since `D' is the default (see `U')
  PC       liblzma.pc
make[2]: Leaving directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma'
make[1]: Leaving directory '/tmp/RtmpxrW7B3/R.INSTALL3d61607b0ae2/gdsfmt/src/XZ/xz-5.2.2/src/liblzma'
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
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -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 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 -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/gdsfmt/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gdsfmt'
    finding HTML links ... done
    add.gdsn                                html  
    addfile.gdsn                            html  
    addfolder.gdsn                          html  
    append.gdsn                             html  
    apply.gdsn                              html  
    assign.gdsn                             html  
    cache.gdsn                              html  
    cleanup.gds                             html  
    closefn.gds                             html  
    clusterApply.gdsn                       html  
    cnt.gdsn                                html  
    compression.gdsn                        html  
    copyto.gdsn                             html  
    createfn.gds                            html  
    delete.attr.gdsn                        html  
    delete.gdsn                             html  
    diagnosis.gds                           html  
    digest.gdsn                             html  
    gds.class                               html  
    gdsfmt-package                          html  
    gdsn.class                              html  
    get.attr.gdsn                           html  
    getfile.gdsn                            html  
    getfolder.gdsn                          html  
    index.gdsn                              html  
    is.element.gdsn                         html  
    lasterr.gds                             html  
    ls.gdsn                                 html  
    moveto.gdsn                             html  
    name.gdsn                               html  
    objdesp.gdsn                            html  
    openfn.gds                              html  
    permdim.gdsn                            html  
    print.gds.class                         html  
    put.attr.gdsn                           html  
    read.gdsn                               html  
    readex.gdsn                             html  
    readmode.gdsn                           html  
    rename.gdsn                             html  
    setdim.gdsn                             html  
    showfile.gds                            html  
    summarize.gdsn                          html  
    sync.gds                                html  
    system.gds                              html  
    write.gdsn                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdsfmt)
Making 'packages.html' ... done