Xiuwen Zheng
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/gdsfmt |
| Branch: RELEASE_3_8 |
| Last Commit: b911b95 |
| Last Changed Date: 2018-11-26 17:40:22 -0400 (Mon, 26 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:24:49 -0400 (Sat, 13 Apr 2019).
| Package 584/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| gdsfmt 1.18.1 Xiuwen Zheng
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: gdsfmt |
| Version: 1.18.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gdsfmt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gdsfmt_1.18.1.tar.gz |
| StartedAt: 2019-04-13 02:24:22 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 02:31:44 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 442.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gdsfmt.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gdsfmt.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings gdsfmt_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package 'gdsfmt' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 6.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/gdsfmt/libs/i386/gdsfmt.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.Rcheck/00check.log'
for details.
gdsfmt.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/gdsfmt_1.18.1.tar.gz && rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gdsfmt.buildbin-libdir gdsfmt_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL gdsfmt_1.18.1.zip && rm gdsfmt_1.18.1.tar.gz gdsfmt_1.18.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2177k 100 2177k 0 0 8357k 0 --:--:-- --:--:-- --:--:-- 8474k
install for i386
* installing *source* package 'gdsfmt' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_CoreArray.cpp -o R_CoreArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c gdsfmt.cpp -o gdsfmt.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c digest.cpp -o digest.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dAny.cpp -o CoreArray/dAny.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dBase.cpp -o CoreArray/dBase.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dFile.cpp -o CoreArray/dFile.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dStream.cpp -o CoreArray/dStream.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/adler32.c -o ZLIB/adler32.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/compress.c -o ZLIB/compress.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/crc32.c -o ZLIB/crc32.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/deflate.c -o ZLIB/deflate.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/infback.c -o ZLIB/infback.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/inffast.c -o ZLIB/inffast.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/inflate.c -o ZLIB/inflate.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/inftrees.c -o ZLIB/inftrees.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/trees.c -o ZLIB/trees.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/uncompr.c -o ZLIB/uncompr.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c ZLIB/zutil.c -o ZLIB/zutil.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4.c -o LZ4/lz4.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4hc.c -o LZ4/lz4hc.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4frame.c -o LZ4/lz4frame.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && unzip -q xz-5.2.3-win.zip
cp XZ/xz-5.2.3/i386/liblzma.a .
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o gdsfmt.dll tmp.def 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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.buildbin-libdir/gdsfmt/libs/i386
** 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
In R CMD INSTALL
install for x64
* installing *source* package 'gdsfmt' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c R_CoreArray.cpp -o R_CoreArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c gdsfmt.cpp -o gdsfmt.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c digest.cpp -o digest.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dAny.cpp -o CoreArray/dAny.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dBase.cpp -o CoreArray/dBase.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dFile.cpp -o CoreArray/dFile.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dStream.cpp -o CoreArray/dStream.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/adler32.c -o ZLIB/adler32.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/compress.c -o ZLIB/compress.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/crc32.c -o ZLIB/crc32.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/deflate.c -o ZLIB/deflate.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/infback.c -o ZLIB/infback.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/inffast.c -o ZLIB/inffast.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/inflate.c -o ZLIB/inflate.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/inftrees.c -o ZLIB/inftrees.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/trees.c -o ZLIB/trees.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/uncompr.c -o ZLIB/uncompr.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c ZLIB/zutil.c -o ZLIB/zutil.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4.c -o LZ4/lz4.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4hc.c -o LZ4/lz4hc.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LZ4/lz4frame.c -o LZ4/lz4frame.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LZ4/xxhash.c -o LZ4/xxhash.o
cd XZ && unzip -q xz-5.2.3-win.zip
cp XZ/xz-5.2.3/x64/liblzma.a .
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o gdsfmt.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/gdsfmt.buildbin-libdir/gdsfmt/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gdsfmt' as gdsfmt_1.18.1.zip
* DONE (gdsfmt)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'gdsfmt' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
gdsfmt.Rcheck/tests_i386/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_i386\test.gds (224B)
+ [ ]
|--+ int { Int32 100, 400B }
\--+ int.matrix { Int32 100x50, 19.5K } *
File: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_i386\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: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_i386\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
1 C:\\Users\\biocbuild\\bbs-3.8-bioc\\meat\\gdsfmt.Rcheck\\tests_i386\\test.gds
ReadOnly State
1 FALSE open
FileName
1 C:\\Users\\biocbuild\\bbs-3.8-bioc\\meat\\gdsfmt.Rcheck\\tests_i386\\test.gds
ReadOnly State
1 FALSE closed
FUNCTION: summarize.gdsn
FUNCTION: sync.gds
FUNCTION: system.gds
FUNCTION: write.gdsn
RUNIT TEST PROTOCOL -- Sat Apr 13 02:28:41 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
144.15 14.64 161.12
|
gdsfmt.Rcheck/tests_x64/runTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_x64\test.gds (224B)
+ [ ]
|--+ int { Int32 100, 400B }
\--+ int.matrix { Int32 100x50, 19.5K } *
File: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_x64\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: C:\Users\biocbuild\bbs-3.8-bioc\meat\gdsfmt.Rcheck\tests_x64\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
1 C:\\Users\\biocbuild\\bbs-3.8-bioc\\meat\\gdsfmt.Rcheck\\tests_x64\\test.gds
ReadOnly State
1 FALSE open
FileName
1 C:\\Users\\biocbuild\\bbs-3.8-bioc\\meat\\gdsfmt.Rcheck\\tests_x64\\test.gds
ReadOnly State
1 FALSE closed
FUNCTION: summarize.gdsn
FUNCTION: sync.gds
FUNCTION: system.gds
FUNCTION: write.gdsn
RUNIT TEST PROTOCOL -- Sat Apr 13 02:31:39 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
160.73 15.71 178.18
|
|
gdsfmt.Rcheck/examples_i386/gdsfmt-Ex.timings
|
gdsfmt.Rcheck/examples_x64/gdsfmt-Ex.timings
|