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CHECK report for gdsfmt on malbec2

This page was generated on 2019-10-16 12:06:02 -0400 (Wed, 16 Oct 2019).

Package 616/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.20.0
Xiuwen Zheng
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/gdsfmt
Branch: RELEASE_3_9
Last Commit: b1fbaba
Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: gdsfmt
Version: 1.20.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gdsfmt_1.20.0.tar.gz
StartedAt: 2019-10-16 01:47:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:50:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:  OK 
CheckDir: gdsfmt.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:gdsfmt.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings gdsfmt_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.20.0’
* 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 ... NOTE
  installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/00check.log’
for details.

Installation output

gdsfmt.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL gdsfmt
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘gdsfmt’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c R_CoreArray.cpp -o R_CoreArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c gdsfmt.cpp -o gdsfmt.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c digest.cpp -o digest.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dAny.cpp -o CoreArray/dAny.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dBase.cpp -o CoreArray/dBase.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dFile.cpp -o CoreArray/dFile.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dStream.cpp -o CoreArray/dStream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/adler32.c -o ZLIB/adler32.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/compress.c -o ZLIB/compress.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/crc32.c -o ZLIB/crc32.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/deflate.c -o ZLIB/deflate.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/infback.c -o ZLIB/infback.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/inffast.c -o ZLIB/inffast.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/inflate.c -o ZLIB/inflate.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/inftrees.c -o ZLIB/inftrees.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/trees.c -o ZLIB/trees.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/uncompr.c -o ZLIB/uncompr.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c ZLIB/zutil.c -o ZLIB/zutil.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c LZ4/lz4.c -o LZ4/lz4.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c LZ4/lz4hc.c -o LZ4/lz4hc.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -c LZ4/lz4frame.c -o LZ4/lz4frame.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray  -I/usr/local/include  -fpic  -g -O2  -Wall -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="gcc" CPP="gcc -E" CXX="g++ -std=gnu++11" CXXCPP="g++ -std=gnu++11 -E" --build="" \
	--with-pic --enable-silent-rules --quiet --disable-xz > /dev/null
cd XZ/xz-5.2.3/src/liblzma && make
make[1]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/src/liblzma'
Making all in api
make[2]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/src/liblzma/api'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/src/liblzma/api'
make[2]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/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-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
lzma/lzma_decoder.c: In function ‘lzma_decode’:
lzma/lzma_decoder.c:577:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
       --limit;
       ^~~~~~~
lzma/lzma_decoder.c:578:6: note: here
      case 4:
      ^~~~
lzma/lzma_decoder.c:583:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
       --limit;
       ^~~~~~~
lzma/lzma_decoder.c:584:6: note: here
      case 3:
      ^~~~
lzma/lzma_decoder.c:589:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
       --limit;
       ^~~~~~~
lzma/lzma_decoder.c:590:6: note: here
      case 2:
      ^~~~
lzma/lzma_decoder.c:595:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
       --limit;
       ^~~~~~~
lzma/lzma_decoder.c:596:6: note: here
      case 1:
      ^~~~
lzma/lzma_decoder.c:354:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
   pos_state = dict.pos & pos_mask;
   ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
lzma/lzma_decoder.c:356:2: note: here
  case SEQ_NORMALIZE:
  ^~~~
In file included from lzma/lzma_decoder.c:17:0:
../../src/liblzma/rangecoder/range_decoder.h:132:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
  prob -= (prob) >> RC_MOVE_BITS; \
lzma/lzma_decoder.c:491:3: note: in expansion of macro ‘rc_update_1’
   rc_update_1(coder->is_match[state][pos_state]);
   ^~~~~~~~~~~
lzma/lzma_decoder.c:493:2: note: here
  case SEQ_IS_REP:
  ^~~~
lzma/lzma_decoder.c:692:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
    if (unlikely(!dict_is_distance_valid(&dict, 0))) {
       ^
lzma/lzma_decoder.c:697:2: note: here
  case SEQ_IS_REP0:
  ^~~~
In file included from lzma/lzma_decoder.c:17:0:
../../src/liblzma/rangecoder/range_decoder.h:132:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
  prob -= (prob) >> RC_MOVE_BITS; \
lzma/lzma_decoder.c:726:5: note: in expansion of macro ‘rc_update_1’
     rc_update_1(coder->is_rep0[state]);
     ^~~~~~~~~~~
lzma/lzma_decoder.c:728:2: note: here
  case SEQ_IS_REP1:
  ^~~~
In file included from lzma/lzma_decoder.c:17:0:
../../src/liblzma/rangecoder/range_decoder.h:132:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
  prob -= (prob) >> RC_MOVE_BITS; \
lzma/lzma_decoder.c:741:6: note: in expansion of macro ‘rc_update_1’
      rc_update_1(coder->is_rep1[state]);
      ^~~~~~~~~~~
lzma/lzma_decoder.c:742:2: note: here
  case SEQ_IS_REP2:
  ^~~~
lzma/lzma_decoder.c:113:9: warning: this statement may fall through [-Wimplicit-fallthrough=]
  symbol = 1; \
  ~~~~~~~^~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
lzma/lzma_decoder.c:114:1: note: here
 case seq ## _CHOICE: \
 ^
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
In file included from lzma/lzma_decoder.c:17:0:
../../src/liblzma/rangecoder/range_decoder.h:132:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
  prob -= (prob) >> RC_MOVE_BITS; \
lzma/lzma_decoder.c:122:3: note: in expansion of macro ‘rc_update_1’
   rc_update_1(ld.choice); \
   ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
lzma/lzma_decoder.c:123:1: note: here
 case seq ## _CHOICE2: \
 ^
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
In file included from lzma/lzma_decoder.c:17:0:
../../src/liblzma/rangecoder/range_decoder.h:132:7: warning: this statement may fall through [-Wimplicit-fallthrough=]
  prob -= (prob) >> RC_MOVE_BITS; \
lzma/lzma_decoder.c:135:4: note: in expansion of macro ‘rc_update_1’
    rc_update_1(ld.choice2); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:136:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH0); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:136:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH0); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:137:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH1); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:137:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH1); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:138:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH2); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:138:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH2); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:139:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH3); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:139:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH3); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:140:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH4); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:140:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH4); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:141:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH5); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:141:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH5); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:142:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH6); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:114:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  if (rc.code < rc_bound)
     ^
../../src/liblzma/rangecoder/range_decoder.h:142:2: note: in expansion of macro ‘rc_if_0’
  rc_if_0(prob, seq) { \
  ^~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:155:2: note: in expansion of macro ‘rc_bit_last’
  rc_bit_last(prob, \
  ^~~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:12: note: in expansion of macro ‘rc_bit’
  case seq: rc_bit(prob, action0, action1, seq)
            ^~~~~~
lzma/lzma_decoder.c:142:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH6); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
../../src/liblzma/rangecoder/range_decoder.h:167:2: note: here
  case seq: rc_bit(prob, action0, action1, seq)
  ^
lzma/lzma_decoder.c:143:4: note: in expansion of macro ‘rc_bit_case’
    rc_bit_case(ld.high[symbol], , , seq ## _HIGH7); \
    ^~~~~~~~~~~
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
lzma/lzma_decoder.c:144:11: warning: this statement may fall through [-Wimplicit-fallthrough=]
    target = symbol - LEN_HIGH_SYMBOLS \
lzma/lzma_decoder.c:769:4: note: in expansion of macro ‘len_decode’
    len_decode(len, coder->rep_len_decoder,
    ^~~~~~~~~~
lzma/lzma_decoder.c:782:2: note: here
  case SEQ_COPY:
  ^~~~
  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 '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/src/liblzma'
make[1]: Leaving directory '/home/biocbuild/bbs-3.9-bioc/meat/gdsfmt/src/XZ/xz-5.2.3/src/liblzma'
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
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/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/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.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 -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-gdsfmt/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gdsfmt)

Tests output

gdsfmt.Rcheck/tests/runTests.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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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' (59.5K)
    # of fragments: 8
    save to 'test.gds.tmp'
    rename 'test.gds.tmp' (59.5K, 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: /home/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds (224B)
+    [  ]
|--+ int   { Int32 100, 400B }
\--+ int.matrix   { Int32 100x50, 19.5K } *
File: /home/biocbuild/bbs-3.9-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: /home/biocbuild/bbs-3.9-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 State
1 /home/biocbuild/bbs-3.9-bioc/meat/gdsfmt.Rcheck/tests/test.gds    FALSE  open
                                                        FileName ReadOnly
1 /home/biocbuild/bbs-3.9-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 -- Wed Oct 16 01:50:38 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 
126.025   7.201 135.099

Example timings

gdsfmt.Rcheck/gdsfmt-Ex.timings

nameusersystemelapsed
add.gdsn0.0930.0040.097
addfile.gdsn0.0080.0000.008
addfolder.gdsn0.0160.0040.020
append.gdsn0.0210.0000.021
apply.gdsn0.0350.0040.039
assign.gdsn0.0210.0000.021
cache.gdsn0.0000.0020.002
cleanup.gds0.0070.0040.011
closefn.gds0.0010.0000.002
clusterApply.gdsn0.0640.0120.882
cnt.gdsn0.0020.0000.002
compression.gdsn0.0040.0000.005
copyto.gdsn0.0210.0040.026
createfn.gds0.0060.0000.005
delete.attr.gdsn0.0010.0030.004
delete.gdsn0.0000.0060.006
diagnosis.gds0.0200.0010.022
digest.gdsn0.0570.0040.061
gdsfmt-package0.0320.0000.032
get.attr.gdsn0.0030.0000.003
getfile.gdsn0.0060.0000.006
getfolder.gdsn0.0220.0080.030
index.gdsn0.0090.0010.010
is.element.gdsn0.0000.0020.003
lasterr.gds000
ls.gdsn0.0020.0000.002
moveto.gdsn0.0330.0000.033
name.gdsn0.0010.0000.001
objdesp.gdsn0.0110.0000.011
openfn.gds0.0060.0000.006
permdim.gdsn0.0080.0020.009
print.gds.class0.0130.0010.015
put.attr.gdsn0.0040.0000.004
read.gdsn0.0090.0040.013
readex.gdsn0.0080.0000.013
readmode.gdsn0.0030.0000.003
rename.gdsn0.0040.0000.004
setdim.gdsn0.0120.0000.012
showfile.gds0.0050.0000.005
summarize.gdsn0.0010.0010.002
sync.gds0.0000.0020.002
system.gds0.0030.0040.006
write.gdsn0.0020.0020.024