Package: gdsfmt

Version: 1.18.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gdsfmt_1.18.1.tar.gz

StartedAt: 2019-04-16 00:04:57 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:08:23 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 205.8 seconds

RetCode: 0

Status:  OK

CheckDir: gdsfmt.Rcheck

Warnings: 0

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gdsfmt_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gdsfmt/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gdsfmt’ version ‘1.18.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gdsfmt’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gdsfmt
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/3.5/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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(test.verbose=FALSE)
> BiocGenerics:::testPackage("gdsfmt")
FUNCTION: add.gdsn
FUNCTION: addfile.gdsn
FUNCTION: addfolder.gdsn
FUNCTION: append.gdsn
FUNCTION: apply.gdsn
[1]  1 11 21 31 41 51
[1]  2 12 22 32 42 52
[1]  3 13 23 33 43 53
[1]  4 14 24 34 44 54
[1]  5 15 25 35 45 55
[1]  6 16 26 36 46 56
[1]  7 17 27 37 47 57
[1]  8 18 28 38 48 58
[1]  9 19 29 39 49 59
[1] 10 20 30 40 50 60
[1]  1 21 41
[1]  3 23 43
[1]  5 25 45
[1]  7 27 47
[1]  9 29 49
index: 1, [1]  1 21 41
index: 2, [1]  3 23 43
index: 3, [1]  5 25 45
index: 4, [1]  7 27 47
index: 5, [1]  9 29 49
index: 1, [1]  1 21 41
index: 3, [1]  3 23 43
index: 5, [1]  5 25 45
index: 7, [1]  7 27 47
index: 9, [1]  9 29 49
[1] "L,1"  "L,11" "L,21" "L,31" "L,41" "L,51"
[1] "L,2"  "L,12" "L,22" "L,32" "L,42" "L,52"
[1] "L,3"  "L,13" "L,23" "L,33" "L,43" "L,53"
[1] "L,4"  "L,14" "L,24" "L,34" "L,44" "L,54"
[1] "L,5"  "L,15" "L,25" "L,35" "L,45" "L,55"
[1] "L,6"  "L,16" "L,26" "L,36" "L,46" "L,56"
[1] "L,7"  "L,17" "L,27" "L,37" "L,47" "L,57"
[1] "L,8"  "L,18" "L,28" "L,38" "L,48" "L,58"
[1] "L,9"  "L,19" "L,29" "L,39" "L,49" "L,59"
[1] "L,10" "L,20" "L,30" "L,40" "L,50" "L,60"
 [1]  1  2  3  4  5  6  7  8  9 10
 [1] 11 12 13 14 15 16 17 18 19 20
 [1] 21 22 23 24 25 26 27 28 29 30
 [1] 31 32 33 34 35 36 37 38 39 40
 [1] 41 42 43 44 45 46 47 48 49 50
 [1] 51 52 53 54 55 56 57 58 59 60
[1] 1 3 5 7 9
[1] 21 23 25 27 29
[1] 41 43 45 47 49
[1] "L,1" "L,3" "L,5" "L,7" "L,9"
[1] "L,21" "L,23" "L,25" "L,27" "L,29"
[1] "L,41" "L,43" "L,45" "L,47" "L,49"
[1]  1 11 NA NA 41 51
[1]  2 12 NA NA 42 52
[1]  3 13 NA NA 43 53
[1]  4 14 NA NA 44 54
[1]  5 15 NA NA 45 55
[1]  6 NA NA NA 46 56
[1]  7 NA NA NA 47 57
[1]  8 NA NA NA 48 58
[1]  9 NA NA NA 49 59
[1] 10 NA NA NA 50 60
 [1]  1  2  3  4  5  6  7  8  9 10
 [1] 11 12 13 14 15 NA NA NA NA NA
 [1] NA NA NA NA NA NA NA NA NA NA
 [1] NA NA NA NA NA NA NA NA NA NA
 [1] 41 42 43 44 45 46 47 48 49 50
 [1] 51 52 53 54 55 56 57 58 59 60
$X
[1]  1 11 21 31 41

$Y
[1] 0.01 0.11 0.21 0.31 0.41

$Z
[1] ABC
Levels: ABC DEF ETD TTT

$X
[1]  2 12 22 32 42

$Y
[1] 0.02 0.12 0.22 0.32 0.42

$Z
[1] DEF
Levels: ABC DEF ETD TTT

$X
[1]  3 13 23 33 43

$Y
[1] 0.03 0.13 0.23 0.33 0.43

$Z
[1] ETD
Levels: ABC DEF ETD TTT

$X
[1]  4 14 24 34 44

$Y
[1] 0.04 0.14 0.24 0.34 0.44

$Z
[1] ABC
Levels: ABC DEF ETD TTT

$X
[1]  5 15 25 35 45

$Y
[1] 0.05 0.15 0.25 0.35 0.45

$Z
[1] DEF
Levels: ABC DEF ETD TTT

$X
[1]  6 16 26 36 46

$Y
[1] 0.06 0.16 0.26 0.36 0.46

$Z
[1] ETD
Levels: ABC DEF ETD TTT

$X
[1]  7 17 27 37 47

$Y
[1] 0.07 0.17 0.27 0.37 0.47

$Z
[1] ABC
Levels: ABC DEF ETD TTT

$X
[1]  8 18 28 38 48

$Y
[1] 0.08 0.18 0.28 0.38 0.48

$Z
[1] DEF
Levels: ABC DEF ETD TTT

$X
[1]  9 19 29 39 49

$Y
[1] 0.09 0.19 0.29 0.39 0.49

$Z
[1] ETD
Levels: ABC DEF ETD TTT

$X
[1] 10 20 30 40 50

$Y
[1] 0.1 0.2 0.3 0.4 0.5

$Z
[1] TTT
Levels: ABC DEF ETD TTT

$X
 [1]  1  2  3  4  5  6  7  8  9 10

$Y
 [1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10

$Z
[1] TRUE

$X
 [1] 11 12 13 14 15 16 17 18 19 20

$Y
 [1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20

$Z
[1] FALSE

$X
 [1] 21 22 23 24 25 26 27 28 29 30

$Y
 [1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30

$Z
[1] TRUE

$X
 [1] 31 32 33 34 35 36 37 38 39 40

$Y
 [1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40

$Z
[1] FALSE

$X
 [1] 41 42 43 44 45 46 47 48 49 50

$Y
 [1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50

$Z
[1] TRUE

$X
 [1]  1  2  3  4  5  6  7  8  9 10

$Y
 [1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10

$Z
[1] NA

$X
 [1] 11 12 13 14 15 16 17 18 19 20

$Y
 [1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20

$Z
[1] FALSE

$X
 [1] 21 22 23 24 25 26 27 28 29 30

$Y
 [1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30

$Z
[1] NA

$X
 [1] 31 32 33 34 NA NA NA NA NA NA

$Y
 [1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40

$Z
[1] FALSE

$X
 [1] NA NA NA NA NA 46 47 48 49 50

$Y
 [1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50

$Z
[1] NA

$X
 [1]  1  2  3  4  5  6  7  8  9 10

$Y
 [1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10

$Z
[1] NA

$X
 [1] 11 12 13 14 15 16 17 18 19 20

$Y
 [1] 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20

$Z
[1] FALSE

$X
 [1] 21 22 23 24 25 26 27 28 29 30

$Y
 [1] 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30

$Z
[1] NA

$X
 [1] 31 32 33 34 NA NA NA NA NA NA

$Y
 [1] 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40

$Z
[1] FALSE

$X
 [1] NA NA NA NA NA 46 47 48 49 50

$Y
 [1] 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50

$Z
[1] NA

$X
[1]  2 22 42

$Y
[1] 0.02 0.22 0.42

$Z
[1] DEF
Levels: ABC DEF ETD TTT

$X
[1]  4 24 44

$Y
[1] 0.04 0.24 0.44

$Z
[1] ABC
Levels: ABC DEF ETD TTT

$X
[1]  6 26 46

$Y
[1] 0.06 0.26 0.46

$Z
[1] ETD
Levels: ABC DEF ETD TTT

$X
[1]  8 28 48

$Y
[1] 0.08 0.28 0.48

$Z
[1] DEF
Levels: ABC DEF ETD TTT

$X
[1] 10 30 50

$Y
[1] 0.1 0.3 0.5

$Z
[1] TTT
Levels: ABC DEF ETD TTT

$X
[1]  2  4  6  8 10

$Y
[1] 0.02 0.04 0.06 0.08 0.10

$Z
[1] TRUE

$X
[1] 22 24 26 28 30

$Y
[1] 0.22 0.24 0.26 0.28 0.30

$Z
[1] TRUE

$X
[1] 42 44 46 48 50

$Y
[1] 0.42 0.44 0.46 0.48 0.50

$Z
[1] TRUE

FUNCTION: assign.gdsn
FUNCTION: cache.gdsn
FUNCTION: cleanup.gds
Clean up the fragments of GDS file:
    open the file 'test.gds' (59.4K)
    # of fragments: 8
    save to 'test.gds.tmp'
    rename 'test.gds.tmp' (59.4K, reduced: 12B)
    # of fragments: 7
FUNCTION: closefn.gds
FUNCTION: clusterApply.gdsn
FUNCTION: cnt.gdsn
FUNCTION: compression.gdsn
FUNCTION: copyto.gdsn
FUNCTION: createfn.gds
FUNCTION: delete.attr.gdsn
FUNCTION: delete.gdsn
FUNCTION: diagnosis.gds
Clean up the fragments of GDS file:
    open the file 'test.gds' (5.2K)
    # of fragments: 5
    save to 'test.gds.tmp'
    rename 'test.gds.tmp' (5.2K, reduced: 12B)
    # of fragments: 4
FUNCTION: digest.gdsn
+ raw1   { Int8 131072, 128.0K } *< md5: d9f2acbc0e4257888758ff6ece5f8411; md5_r: d9f2acbc0e4257888758ff6ece5f8411; sha1: daf4efc3cf7278062825d7e4798142baf8ab4aba; sha256: a5b212f05fa19517c71de0853b69f984e4cc50bc4457d1ad7a78d21a8d313fe6; sha512: a55d41e3a09355ad937014a58269d90fdf2a609944ef3b3d9d2033add3a4d8b108d573c1a541fb6c06e1d53d35a6a24180fb2abe6df3e9238fdd9397e8c5edb1
+ raw1   { Int8 131072, 128.0K }
FUNCTION: gds.class
FUNCTION: gdsfmt-package
 [1]  1  2  3  4  5  6  7  8  9 10
 [1] 11 12 13 14 15 16 17 18 19 20
 [1] 21 22 23 24 25 26 27 28 29 30
 [1] 31 32 33 34 35 36 37 38 39 40
 [1] 41 42 43 44 45 46 47 48 49 50
 [1] 51 52 53 54 55 56 57 58 59 60
[1] 1 3 5 7 9
[1] 21 23 25 27 29
[1] 41 43 45 47 49
FUNCTION: gdsn.class
FUNCTION: get.attr.gdsn
FUNCTION: getfile.gdsn
FUNCTION: getfolder.gdsn
FUNCTION: index.gdsn
FUNCTION: is.element.gdsn
FUNCTION: lasterr.gds
FUNCTION: ls.gdsn
FUNCTION: moveto.gdsn
FUNCTION: name.gdsn
FUNCTION: objdesp.gdsn
FUNCTION: openfn.gds
FUNCTION: permdim.gdsn
Clean up the fragments of GDS file:
    open the file 'test.gds' (1.1K)
    # of fragments: 8
    save to 'test.gds.tmp'
    rename 'test.gds.tmp' (726B, reduced: 351B)
    # of fragments: 5
FUNCTION: print.gds.class
File: /Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/tests/test.gds (224B)
+    [  ]
|--+ int   { Int32 100, 400B }
\--+ int.matrix   { Int32 100x50, 19.5K } *
File: /Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/tests/test.gds (20.3K)
+    [  ]
|--+ int   { Int32 100, 400B }
\--+ int.matrix   { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
File: /Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/tests/test.gds (20.3K)
+    [  ]
|--+ int   { Int32 100, 400B }
\--+ int.matrix   { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
+ int   { Int32 100, 400B }
Preview:
  1
  2
  3
  4
  5
  6
...
 95
 96
 97
 98
 99
100
+ int.matrix   { Int32 100x50, 19.5K } *< int: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10
Preview:
   1  101  201  301  401  501 .. 4401 4501 4601 4701 4801 4901
   2  102  202  302  402  502 .. 4402 4502 4602 4702 4802 4902
   3  103  203  303  403  503 .. 4403 4503 4603 4703 4803 4903
   4  104  204  304  404  504 .. 4404 4504 4604 4704 4804 4904
   5  105  205  305  405  505 .. 4405 4505 4605 4705 4805 4905
   6  106  206  306  406  506 .. 4406 4506 4606 4706 4806 4906
......            
  95  195  295  395  495  595 .. 4495 4595 4695 4795 4895 4995
  96  196  296  396  496  596 .. 4496 4596 4696 4796 4896 4996
  97  197  297  397  497  597 .. 4497 4597 4697 4797 4897 4997
  98  198  298  398  498  598 .. 4498 4598 4698 4798 4898 4998
  99  199  299  399  499  599 .. 4499 4599 4699 4799 4899 4999
 100  200  300  400  500  600 .. 4500 4600 4700 4800 4900 5000
FUNCTION: put.attr.gdsn
FUNCTION: read.gdsn
FUNCTION: readex.gdsn
FUNCTION: readmode.gdsn
FUNCTION: rename.gdsn
FUNCTION: setdim.gdsn
FUNCTION: showfile.gds
                                                         FileName ReadOnly
1 /Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/tests/test.gds    FALSE
  State
1  open
                                                         FileName ReadOnly
1 /Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/tests/test.gds    FALSE
   State
1 closed
FUNCTION: summarize.gdsn
FUNCTION: sync.gds
FUNCTION: system.gds
FUNCTION: write.gdsn


RUNIT TEST PROTOCOL -- Tue Apr 16 00:08:15 2019 
*********************************************** 
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
gdsfmt RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
143.183  17.293 162.755 

name	user	system	elapsed
add.gdsn	0.103	0.011	0.119
addfile.gdsn	0.006	0.002	0.009
addfolder.gdsn	0.029	0.003	0.033
append.gdsn	0.021	0.002	0.024
apply.gdsn	0.050	0.013	0.063
assign.gdsn	0.027	0.005	0.032
cache.gdsn	0.004	0.001	0.005
cleanup.gds	0.018	0.003	0.022
closefn.gds	0.002	0.001	0.005
clusterApply.gdsn	0.055	0.015	0.790
cnt.gdsn	0.003	0.001	0.003
compression.gdsn	0.010	0.002	0.012
copyto.gdsn	0.033	0.002	0.035
createfn.gds	0.006	0.001	0.007
delete.attr.gdsn	0.004	0.000	0.005
delete.gdsn	0.012	0.001	0.012
diagnosis.gds	0.018	0.002	0.020
digest.gdsn	0.063	0.008	0.072
gdsfmt-package	0.042	0.006	0.048
get.attr.gdsn	0.004	0.001	0.005
getfile.gdsn	0.006	0.003	0.010
getfolder.gdsn	0.028	0.002	0.030
index.gdsn	0.013	0.001	0.015
is.element.gdsn	0.003	0.001	0.006
lasterr.gds	0	0	0
ls.gdsn	0.003	0.001	0.004
moveto.gdsn	0.044	0.003	0.053
name.gdsn	0.002	0.001	0.007
objdesp.gdsn	0.009	0.002	0.012
openfn.gds	0.008	0.002	0.010
permdim.gdsn	0.014	0.002	0.016
print.gds.class	0.013	0.001	0.014
put.attr.gdsn	0.004	0.001	0.005
read.gdsn	0.014	0.002	0.017
readex.gdsn	0.009	0.003	0.011
readmode.gdsn	0.004	0.001	0.005
rename.gdsn	0.006	0.001	0.007
setdim.gdsn	0.015	0.003	0.019
showfile.gds	0.007	0.001	0.008
summarize.gdsn	0.005	0.002	0.008
sync.gds	0.004	0.001	0.005
system.gds	0.008	0.001	0.009
write.gdsn	0.004	0.001	0.006